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1.  M3: an improved SNP calling algorithm for Illumina BeadArray data 
Bioinformatics  2011;28(3):358-365.
Summary: Genotype calling from high-throughput platforms such as Illumina and Affymetrix is a critical step in data processing, so that accurate information on genetic variants can be obtained for phenotype–genotype association studies. A number of algorithms have been developed to infer genotypes from data generated through the Illumina BeadStation platform, including GenCall, GenoSNP, Illuminus and CRLMM. Most of these algorithms are built on population-based statistical models to genotype every SNP in turn, such as GenCall with the GenTrain clustering algorithm, and require a large reference population to perform well. These approaches may not work well for rare variants where only a small proportion of the individuals carry the variant. A fundamentally different approach, implemented in GenoSNP, adopts a single nucleotide polymorphism (SNP)-based model to infer genotypes of all the SNPs in one individual, making it an appealing alternative to call rare variants. However, compared to the population-based strategies, more SNPs in GenoSNP may fail the Hardy–Weinberg Equilibrium test. To take advantage of both strategies, we propose a two-stage SNP calling procedure, named the modified mixture model (M3), to improve call accuracy for both common and rare variants. The effectiveness of our approach is demonstrated through applications to genotype calling on a set of HapMap samples used for quality control purpose in a large case–control study of cocaine dependence. The increase in power with M3 is greater for rare variants than for common variants depending on the model.
Availability: M3 algorithm: http://bioinformatics.med.yale.edu/group.
Contact: name@bio.com; hongyu.zhao@yale.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btr673
PMCID: PMC3268244  PMID: 22155947
2.  Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms 
BMC Genomics  2014;15:16.
Background
High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome complexity, i.e. investigating only parts of the genome, is reduced-representation library (RRL) sequencing. Like similar approaches, RRL sequencing reduces ascertainment bias due to simultaneous discovery and genotyping of single-nucleotide polymorphisms (SNPs) and does not require reference genomes. Yet, generating such datasets remains challenging due to laboratory and bioinformatical issues. In the laboratory, current protocols require improvements with regards to sequencing homologous fragments to reduce the number of missing genotypes. From the bioinformatical perspective, the reliance of most studies on a single SNP caller disregards the possibility that different algorithms may produce disparate SNP datasets.
Results
We present an improved RRL (iRRL) protocol that maximizes the generation of homologous DNA sequences, thus achieving improved genotyping-by-sequencing efficiency. Our modifications facilitate generation of single-sample libraries, enabling individual genotype assignments instead of pooled-sample analysis. We sequenced ~1% of the orangutan genome with 41-fold median coverage in 31 wild-born individuals from two populations. SNPs and genotypes were called using three different algorithms. We obtained substantially different SNP datasets depending on the SNP caller. Genotype validations revealed that the Unified Genotyper of the Genome Analysis Toolkit and SAMtools performed significantly better than a caller from CLC Genomics Workbench (CLC). Of all conflicting genotype calls, CLC was only correct in 17% of the cases. Furthermore, conflicting genotypes between two algorithms showed a systematic bias in that one caller almost exclusively assigned heterozygotes, while the other one almost exclusively assigned homozygotes.
Conclusions
Our enhanced iRRL approach greatly facilitates genotyping-by-sequencing and thus direct estimates of allele frequencies. Our direct comparison of three commonly used SNP callers emphasizes the need to question the accuracy of SNP and genotype calling, as we obtained considerably different SNP datasets depending on caller algorithms, sequencing depths and filtering criteria. These differences affected scans for signatures of natural selection, but will also exert undue influences on demographic inferences. This study presents the first effort to generate a population genomic dataset for wild-born orangutans with known population provenance.
doi:10.1186/1471-2164-15-16
PMCID: PMC3897891  PMID: 24405840
Next-generation sequencing; Single-nucleotide polymorphisms; Reduced-representation libraries; Bioinformatics; GATK; SAMtools; CLC genomics workbench; Great apes
3.  A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies 
PLoS Genetics  2009;5(6):e1000529.
Genotype imputation methods are now being widely used in the analysis of genome-wide association studies. Most imputation analyses to date have used the HapMap as a reference dataset, but new reference panels (such as controls genotyped on multiple SNP chips and densely typed samples from the 1,000 Genomes Project) will soon allow a broader range of SNPs to be imputed with higher accuracy, thereby increasing power. We describe a genotype imputation method (IMPUTE version 2) that is designed to address the challenges presented by these new datasets. The main innovation of our approach is a flexible modelling framework that increases accuracy and combines information across multiple reference panels while remaining computationally feasible. We find that IMPUTE v2 attains higher accuracy than other methods when the HapMap provides the sole reference panel, but that the size of the panel constrains the improvements that can be made. We also find that imputation accuracy can be greatly enhanced by expanding the reference panel to contain thousands of chromosomes and that IMPUTE v2 outperforms other methods in this setting at both rare and common SNPs, with overall error rates that are 15%–20% lower than those of the closest competing method. One particularly challenging aspect of next-generation association studies is to integrate information across multiple reference panels genotyped on different sets of SNPs; we show that our approach to this problem has practical advantages over other suggested solutions.
Author Summary
Large association studies have proven to be effective tools for identifying parts of the genome that influence disease risk and other heritable traits. So-called “genotype imputation” methods form a cornerstone of modern association studies: by extrapolating genetic correlations from a densely characterized reference panel to a sparsely typed study sample, such methods can estimate unobserved genotypes with high accuracy, thereby increasing the chances of finding true associations. To date, most genome-wide imputation analyses have used reference data from the International HapMap Project. While this strategy has been successful, association studies in the near future will also have access to additional reference information, such as control sets genotyped on multiple SNP chips and dense genome-wide haplotypes from the 1,000 Genomes Project. These new reference panels should improve the quality and scope of imputation, but they also present new methodological challenges. We describe a genotype imputation method, IMPUTE version 2, that is designed to address these challenges in next-generation association studies. We show that our method can use a reference panel containing thousands of chromosomes to attain higher accuracy than is possible with the HapMap alone, and that our approach is more accurate than competing methods on both current and next-generation datasets. We also highlight the modeling issues that arise in imputation datasets.
doi:10.1371/journal.pgen.1000529
PMCID: PMC2689936  PMID: 19543373
4.  Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips 
BMC Bioinformatics  2011;12:68.
Background
Illumina's Infinium SNP BeadChips are extensively used in both small and large-scale genetic studies. A fundamental step in any analysis is the processing of raw allele A and allele B intensities from each SNP into genotype calls (AA, AB, BB). Various algorithms which make use of different statistical models are available for this task. We compare four methods (GenCall, Illuminus, GenoSNP and CRLMM) on data where the true genotypes are known in advance and data from a recently published genome-wide association study.
Results
In general, differences in accuracy are relatively small between the methods evaluated, although CRLMM and GenoSNP were found to consistently outperform GenCall. The performance of Illuminus is heavily dependent on sample size, with lower no call rates and improved accuracy as the number of samples available increases. For X chromosome SNPs, methods with sex-dependent models (Illuminus, CRLMM) perform better than methods which ignore gender information (GenCall, GenoSNP). We observe that CRLMM and GenoSNP are more accurate at calling SNPs with low minor allele frequency than GenCall or Illuminus. The sample quality metrics from each of the four methods were found to have a high level of agreement at flagging samples with unusual signal characteristics.
Conclusions
CRLMM, GenoSNP and GenCall can be applied with confidence in studies of any size, as their performance was shown to be invariant to the number of samples available. Illuminus on the other hand requires a larger number of samples to achieve comparable levels of accuracy and its use in smaller studies (50 or fewer individuals) is not recommended.
doi:10.1186/1471-2105-12-68
PMCID: PMC3063825  PMID: 21385424
5.  SNiPer: Improved SNP genotype calling for Affymetrix 10K GeneChip microarray data 
BMC Genomics  2005;6:149.
Background
High throughput microarray-based single nucleotide polymorphism (SNP) genotyping has revolutionized the way genome-wide linkage scans and association analyses are performed. One of the key features of the array-based GeneChip® Mapping 10K Array from Affymetrix is the automated SNP calling algorithm. The Affymetrix algorithm was trained on a database of ethnically diverse DNA samples to create SNP call zones that are used as static models to make genotype calls for experimental data. We describe here the implementation of clustering algorithms on large training datasets resulting in improved SNP call rates on the 10K GeneChip.
Results
A database of 948 individuals genotyped on the GeneChip® Mapping 10K 2.0 Array was used to identify 822 SNPs that were called consistently less than 75% of the time. These SNPs represent on average 8.25% of the total SNPs on each chromosome with chromosome 19, the most gene-rich chromosome, containing the highest proportion of poor performers (18.7%). To remedy this, we created SNiPer, a new application which uses two clustering algorithms to yield increased call rates and equivalent concordance to Affymetrix called genotypes. We include a training set for these algorithms based on individual genotypes for 705 samples. SNiPer has the capability to be retrained for lab-specific training sets. SNiPer is freely available for download at .
Conclusion
The correct calling of poor performing SNPs may prove to be key in future linkage studies performed on the 10K GeneChip. It would prove particularly invaluable for those diseases that map to chromosome 19, known to contain a high proportion of poorly performing SNPs. Our results illustrate that SNiPer can be used to increase call rates on the 10K GeneChip® without sacrificing accuracy, thereby increasing the amount of valid data generated.
doi:10.1186/1471-2164-6-149
PMCID: PMC1280925  PMID: 16262895
6.  HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data 
PLoS Computational Biology  2014;10(3):e1003502.
As the more recent next-generation sequencing (NGS) technologies provide longer read sequences, the use of sequencing datasets for complete haplotype phasing is fast becoming a reality, allowing haplotype reconstruction of a single sequenced genome. Nearly all previous haplotype reconstruction studies have focused on diploid genomes and are rarely scalable to genomes with higher ploidy. Yet computational investigations into polyploid genomes carry great importance, impacting plant, yeast and fish genomics, as well as the studies of the evolution of modern-day eukaryotes and (epi)genetic interactions between copies of genes. In this paper, we describe a novel maximum-likelihood estimation framework, HapTree, for polyploid haplotype assembly of an individual genome using NGS read datasets. We evaluate the performance of HapTree on simulated polyploid sequencing read data modeled after Illumina sequencing technologies. For triploid and higher ploidy genomes, we demonstrate that HapTree substantially improves haplotype assembly accuracy and efficiency over the state-of-the-art; moreover, HapTree is the first scalable polyplotyping method for higher ploidy. As a proof of concept, we also test our method on real sequencing data from NA12878 (1000 Genomes Project) and evaluate the quality of assembled haplotypes with respect to trio-based diplotype annotation as the ground truth. The results indicate that HapTree significantly improves the switch accuracy within phased haplotype blocks as compared to existing haplotype assembly methods, while producing comparable minimum error correction (MEC) values. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2–5.
Author Summary
While human and other eukaryotic genomes typically contain two copies of every chromosome, plants, yeast and fish such as salmon can have strictly more than two copies of each chromosome. By running standard genotype calling tools, it is possible to accurately identify the number of “wild type” and “mutant” alleles (A, C, G, or T) for each single-nucleotide polymorphism (SNP) site. However, in the case of two heterozygous SNP sites, genotype calling tools cannot determine whether “mutant” alleles from different SNP loci are on the same or different chromosomes. While the former would be healthy, in many cases the latter can cause loss of function; it is therefore necessary to identify the phase—the copies of a chromosome on which the mutant alleles occur—in addition to the genotype. This necessitates efficient algorithms to obtain accurate and comprehensive phase information directly from the next-generation-sequencing read data in higher ploidy species. We introduce an efficient statistical method for this task and show that our method significantly outperforms previous ones, in both accuracy and speed, for phasing triploid and higher ploidy genomes. Our method performs well on human diploid genomes as well, as demonstrated by our improved phasing of the well known NA12878 (1000 Genomes Project).
doi:10.1371/journal.pcbi.1003502
PMCID: PMC3967924  PMID: 24675685
7.  Using Whole-Genome Sequence Data to Predict Quantitative Trait Phenotypes in Drosophila melanogaster 
PLoS Genetics  2012;8(5):e1002685.
Predicting organismal phenotypes from genotype data is important for plant and animal breeding, medicine, and evolutionary biology. Genomic-based phenotype prediction has been applied for single-nucleotide polymorphism (SNP) genotyping platforms, but not using complete genome sequences. Here, we report genomic prediction for starvation stress resistance and startle response in Drosophila melanogaster, using ∼2.5 million SNPs determined by sequencing the Drosophila Genetic Reference Panel population of inbred lines. We constructed a genomic relationship matrix from the SNP data and used it in a genomic best linear unbiased prediction (GBLUP) model. We assessed predictive ability as the correlation between predicted genetic values and observed phenotypes by cross-validation, and found a predictive ability of 0.239±0.008 (0.230±0.012) for starvation resistance (startle response). The predictive ability of BayesB, a Bayesian method with internal SNP selection, was not greater than GBLUP. Selection of the 5% SNPs with either the highest absolute effect or variance explained did not improve predictive ability. Predictive ability decreased only when fewer than 150,000 SNPs were used to construct the genomic relationship matrix. We hypothesize that predictive power in this population stems from the SNP–based modeling of the subtle relationship structure caused by long-range linkage disequilibrium and not from population structure or SNPs in linkage disequilibrium with causal variants. We discuss the implications of these results for genomic prediction in other organisms.
Author Summary
The ability to accurately predict values of complex phenotypes from genotype data will revolutionize plant and animal breeding, personalized medicine, and evolutionary biology. To date, genomic prediction has utilized high-density single-nucleotide polymorphism (SNP) genotyping arrays, but the availability of sequence data opens new frontiers for genomic prediction methods. This article is the first application of genomic phenotype prediction using whole-genome sequence data in a substantial sample of a higher eukaryote. We use ∼2.5 million SNPs with minor allele frequency greater than 2.5% derived from genomic sequences of the “Drosophila Genetic Reference Panel” to predict phenotypes for two traits, starvation resistance and startle-induced locomotor behavior. We systematically address prediction within versus across sexes, genomic best linear unbiased prediction (GBLUP) versus a Bayesian approach, and the effect of SNP density. We find that (i) genomic prediction can be efficiently implemented using sequence data via GBLUP, (ii) there is little gain in predictive ability if the number of SNPs is increased above 150,000, and (iii) neither implicit nor explicit marker selection substantially improves the predictive ability. Although the findings must be seen against the background of small sample sizes, the results illustrate both the potential of the approach and the challenges ahead.
doi:10.1371/journal.pgen.1002685
PMCID: PMC3342952  PMID: 22570636
8.  Imputation of high-density genotypes in the Fleckvieh cattle population 
Background
Currently, genome-wide evaluation of cattle populations is based on SNP-genotyping using ~ 54 000 SNP. Increasing the number of markers might improve genomic predictions and power of genome-wide association studies. Imputation of genotypes makes it possible to extrapolate genotypes from lower to higher density arrays based on a representative reference sample for which genotypes are obtained at higher density.
Methods
Genotypes using 639 214 SNP were available for 797 bulls of the Fleckvieh cattle breed. The data set was divided into a reference and a validation population. Genotypes for all SNP except those included in the BovineSNP50 Bead chip were masked and subsequently imputed for animals of the validation population. Imputation of genotypes was performed with Beagle, findhap.f90, MaCH and Minimac. The accuracy of the imputed genotypes was assessed for four different scenarios including 50, 100, 200 and 400 animals as reference population. The reference animals were selected to account for 78.03%, 89.21%, 97.47% and > 99% of the gene pool of the genotyped population, respectively.
Results
Imputation accuracy increased as the number of animals and relatives in the reference population increased. Population-based algorithms provided highly reliable imputation of genotypes, even for scenarios with 50 and 100 reference animals only. Using MaCH and Minimac, the correlation between true and imputed genotypes was > 0.975 with 100 reference animals only. Pre-phasing the genotypes of both the reference and validation populations not only provided highly accurate imputed genotypes but was also computationally efficient. Genome-wide analysis of imputation accuracy led to the identification of many misplaced SNP.
Conclusions
Genotyping key animals at high density and subsequent population-based genotype imputation yield high imputation accuracy. Pre-phasing the genotypes of the reference and validation populations is computationally efficient and results in high imputation accuracy, even when the reference population is small.
doi:10.1186/1297-9686-45-3
PMCID: PMC3598996  PMID: 23406470
9.  Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies 
BMC Genetics  2009;10:27.
Background
Although high-throughput genotyping arrays have made whole-genome association studies (WGAS) feasible, only a small proportion of SNPs in the human genome are actually surveyed in such studies. In addition, various SNP arrays assay different sets of SNPs, which leads to challenges in comparing results and merging data for meta-analyses. Genome-wide imputation of untyped markers allows us to address these issues in a direct fashion.
Methods
384 Caucasian American liver donors were genotyped using Illumina 650Y (Ilmn650Y) arrays, from which we also derived genotypes from the Ilmn317K array. On these data, we compared two imputation methods: MACH and BEAGLE. We imputed 2.5 million HapMap Release22 SNPs, and conducted GWAS on ~40,000 liver mRNA expression traits (eQTL analysis). In addition, 200 Caucasian American and 200 African American subjects were genotyped using the Affymetrix 500 K array plus a custom 164 K fill-in chip. We then imputed the HapMap SNPs and quantified the accuracy by randomly masking observed SNPs.
Results
MACH and BEAGLE perform similarly with respect to imputation accuracy. The Ilmn650Y results in excellent imputation performance, and it outperforms Affx500K or Ilmn317K sets. For Caucasian Americans, 90% of the HapMap SNPs were imputed at 98% accuracy. As expected, imputation of poorly tagged SNPs (untyped SNPs in weak LD with typed markers) was not as successful. It was more challenging to impute genotypes in the African American population, given (1) shorter LD blocks and (2) admixture with Caucasian populations in this population. To address issue (2), we pooled HapMap CEU and YRI data as an imputation reference set, which greatly improved overall performance. The approximate 40,000 phenotypes scored in these populations provide a path to determine empirically how the power to detect associations is affected by the imputation procedures. That is, at a fixed false discovery rate, the number of cis-eQTL discoveries detected by various methods can be interpreted as their relative statistical power in the GWAS. In this study, we find that imputation offer modest additional power (by 4%) on top of either Ilmn317K or Ilmn650Y, much less than the power gain from Ilmn317K to Ilmn650Y (13%).
Conclusion
Current algorithms can accurately impute genotypes for untyped markers, which enables researchers to pool data between studies conducted using different SNP sets. While genotyping itself results in a small error rate (e.g. 0.5%), imputing genotypes is surprisingly accurate. We found that dense marker sets (e.g. Ilmn650Y) outperform sparser ones (e.g. Ilmn317K) in terms of imputation yield and accuracy. We also noticed it was harder to impute genotypes for African American samples, partially due to population admixture, although using a pooled reference boosts performance. Interestingly, GWAS carried out using imputed genotypes only slightly increased power on top of assayed SNPs. The reason is likely due to adding more markers via imputation only results in modest gain in genetic coverage, but worsens the multiple testing penalties. Furthermore, cis-eQTL mapping using dense SNP set derived from imputation achieves great resolution, and locate associate peak closer to causal variants than conventional approach.
doi:10.1186/1471-2156-10-27
PMCID: PMC2709633  PMID: 19531258
10.  Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples 
BMC Bioinformatics  2008;9(Suppl 9):S17.
Background
Genome-wide association studies (GWAS) aim to identify genetic variants (usually single nucleotide polymorphisms [SNPs]) across the entire human genome that are associated with phenotypic traits such as disease status and drug response. Highly accurate and reproducible genotype calling are paramount since errors introduced by calling algorithms can lead to inflation of false associations between genotype and phenotype. Most genotype calling algorithms currently used for GWAS are based on multiple arrays. Because hundreds of gigabytes (GB) of raw data are generated from a GWAS, the samples are typically partitioned into batches containing subsets of the entire dataset for genotype calling. High call rates and accuracies have been achieved. However, the effects of batch size (i.e., number of chips analyzed together) and of batch composition (i.e., the choice of chips in a batch) on call rate and accuracy as well as the propagation of the effects into significantly associated SNPs identified have not been investigated. In this paper, we analyzed both the batch size and batch composition for effects on the genotype calling algorithm BRLMM using raw data of 270 HapMap samples analyzed with the Affymetrix Human Mapping 500 K array set.
Results
Using data from 270 HapMap samples interrogated with the Affymetrix Human Mapping 500 K array set, three different batch sizes and three different batch compositions were used for genotyping using the BRLMM algorithm. Comparative analysis of the calling results and the corresponding lists of significant SNPs identified through association analysis revealed that both batch size and composition affected genotype calling results and significantly associated SNPs. Batch size and batch composition effects were more severe on samples and SNPs with lower call rates than ones with higher call rates, and on heterozygous genotype calls compared to homozygous genotype calls.
Conclusion
Batch size and composition affect the genotype calling results in GWAS using BRLMM. The larger the differences in batch sizes, the larger the effect. The more homogenous the samples in the batches, the more consistent the genotype calls. The inconsistency propagates to the lists of significantly associated SNPs identified in downstream association analysis. Thus, uniform and large batch sizes should be used to make genotype calls for GWAS. In addition, samples of high homogeneity should be placed into the same batch.
doi:10.1186/1471-2105-9-S9-S17
PMCID: PMC2537568  PMID: 18793462
11.  From Disease Association to Risk Assessment: An Optimistic View from Genome-Wide Association Studies on Type 1 Diabetes 
PLoS Genetics  2009;5(10):e1000678.
Genome-wide association studies (GWAS) have been fruitful in identifying disease susceptibility loci for common and complex diseases. A remaining question is whether we can quantify individual disease risk based on genotype data, in order to facilitate personalized prevention and treatment for complex diseases. Previous studies have typically failed to achieve satisfactory performance, primarily due to the use of only a limited number of confirmed susceptibility loci. Here we propose that sophisticated machine-learning approaches with a large ensemble of markers may improve the performance of disease risk assessment. We applied a Support Vector Machine (SVM) algorithm on a GWAS dataset generated on the Affymetrix genotyping platform for type 1 diabetes (T1D) and optimized a risk assessment model with hundreds of markers. We subsequently tested this model on an independent Illumina-genotyped dataset with imputed genotypes (1,008 cases and 1,000 controls), as well as a separate Affymetrix-genotyped dataset (1,529 cases and 1,458 controls), resulting in area under ROC curve (AUC) of ∼0.84 in both datasets. In contrast, poor performance was achieved when limited to dozens of known susceptibility loci in the SVM model or logistic regression model. Our study suggests that improved disease risk assessment can be achieved by using algorithms that take into account interactions between a large ensemble of markers. We are optimistic that genotype-based disease risk assessment may be feasible for diseases where a notable proportion of the risk has already been captured by SNP arrays.
Author Summary
An often touted utility of genome-wide association studies (GWAS) is that the resulting discoveries can facilitate implementation of personalized medicine, in which preventive and therapeutic interventions for complex diseases can be tailored to individual genetic profiles. However, recent studies using whole-genome SNP genotype data for disease risk assessment have generally failed to achieve satisfactory results, leading to a pessimistic view of the utility of genotype data for such purposes. Here we propose that sophisticated machine-learning approaches on a large ensemble of markers, which contain both confirmed and as yet unconfirmed disease susceptibility variants, may improve the performance of disease risk assessment. We tested an algorithm called Support Vector Machine (SVM) on three large-scale datasets for type 1 diabetes and demonstrated that risk assessment can be highly accurate for the disease. Our results suggest that individualized disease risk assessment using whole-genome data may be more successful for some diseases (such as T1D) than other diseases. However, the predictive accuracy will be dependent on the heritability of the disease under study, the proportion of the genetic risk that is known, and that the right set of markers and right algorithms are being used.
doi:10.1371/journal.pgen.1000678
PMCID: PMC2748686  PMID: 19816555
12.  Cheek swabs, SNP chips, and CNVs: Assessing the quality of copy number variant calls generated with subject-collected mail-in buccal brush DNA samples on a high-density genotyping microarray 
BMC Medical Genetics  2012;13:51.
Background
Multiple investigators have established the feasibility of using buccal brush samples to genotype single nucleotide polymorphisms (SNPs) with high-density genome-wide microarrays, but there is currently no consensus on the accuracy of copy number variants (CNVs) inferred from these data. Regardless of the source of DNA, it is more difficult to detect CNVs than to genotype SNPs using these microarrays, and it therefore remains an open question whether buccal brush samples provide enough high-quality DNA for this purpose.
Methods
To demonstrate the quality of CNV calls generated from DNA extracted from buccal samples, compared to calls generated from blood samples, we evaluated the concordance of calls from individuals who provided both sample types. The Illumina Human660W-Quad BeadChip was used to determine SNPs and CNVs of 39 Arkansas participants in the National Birth Defects Prevention Study (NBDPS), including 16 mother-infant dyads, who provided both whole blood and buccal brush DNA samples.
Results
We observed a 99.9% concordance rate of SNP calls in the 39 blood–buccal pairs. From the same dataset, we performed a similar analysis of CNVs. Each of the 78 samples was independently segmented into regions of like copy number using the Optimal Segmentation algorithm of Golden Helix SNP & Variation Suite 7.
Across 640,663 loci on 22 autosomal chromosomes, segment-mean log R ratios had an average correlation of 0.899 between blood-buccal pairs of samples from the same individual, while the average correlation between all possible blood-buccal pairs of samples from unrelated individuals was 0.318. An independent analysis using the QuantiSNP algorithm produced average correlations of 0.943 between blood-buccal pairs from the same individual versus 0.332 between samples from unrelated individuals.
Segment-mean log R ratios had an average correlation of 0.539 between mother-offspring dyads of buccal samples, which was not statistically significantly different than the average correlation of 0.526 between mother-offspring dyads of blood samples (p=0.302).
Conclusions
We observed performance from the subject-collected mail-in buccal brush samples comparable to that of blood. These results show that such DNA samples can be used for genome-wide scans of both SNPs and CNVs, and that high rates of CNV concordance were achieved whether using a change-point-based algorithm or one based on a hidden Markov model (HMM).
doi:10.1186/1471-2350-13-51
PMCID: PMC3506514  PMID: 22734463
SNPs, Single nucleotide polymorphisms; CNVs, Copy number variants; NBDPS, National Birth Defects Prevention Study; Buccal brush
13.  FastTagger: an efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium 
BMC Bioinformatics  2010;11:66.
Background
Human genome contains millions of common single nucleotide polymorphisms (SNPs) and these SNPs play an important role in understanding the association between genetic variations and human diseases. Many SNPs show correlated genotypes, or linkage disequilibrium (LD), thus it is not necessary to genotype all SNPs for association study. Many algorithms have been developed to find a small subset of SNPs called tag SNPs that are sufficient to infer all the other SNPs. Algorithms based on the r2 LD statistic have gained popularity because r2 is directly related to statistical power to detect disease associations. Most of existing r2 based algorithms use pairwise LD. Recent studies show that multi-marker LD can help further reduce the number of tag SNPs. However, existing tag SNP selection algorithms based on multi-marker LD are both time-consuming and memory-consuming. They cannot work on chromosomes containing more than 100 k SNPs using length-3 tagging rules.
Results
We propose an efficient algorithm called FastTagger to calculate multi-marker tagging rules and select tag SNPs based on multi-marker LD. FastTagger uses several techniques to reduce running time and memory consumption. Our experiment results show that FastTagger is several times faster than existing multi-marker based tag SNP selection algorithms, and it consumes much less memory at the same time. As a result, FastTagger can work on chromosomes containing more than 100 k SNPs using length-3 tagging rules.
FastTagger also produces smaller sets of tag SNPs than existing multi-marker based algorithms, and the reduction ratio ranges from 3%-9% when length-3 tagging rules are used. The generated tagging rules can also be used for genotype imputation. We studied the prediction accuracy of individual rules, and the average accuracy is above 96% when r2 ≥ 0.9.
Conclusions
Generating multi-marker tagging rules is a computation intensive task, and it is the bottleneck of existing multi-marker based tag SNP selection methods. FastTagger is a practical and scalable algorithm to solve this problem.
doi:10.1186/1471-2105-11-66
PMCID: PMC3098109  PMID: 20113476
14.  Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study 
PLoS Medicine  2013;10(2):e1001387.
In an outbreak investigation of Mycobacterium tuberculosis comparing whole genome sequencing (WGS) with traditional genotyping, Stefan Niemann and colleagues found that classical genotyping falsely clustered some strains, and WGS better reflected contact tracing.
Background
Understanding Mycobacterium tuberculosis (Mtb) transmission is essential to guide efficient tuberculosis control strategies. Traditional strain typing lacks sufficient discriminatory power to resolve large outbreaks. Here, we tested the potential of using next generation genome sequencing for identification of outbreak-related transmission chains.
Methods and Findings
During long-term (1997 to 2010) prospective population-based molecular epidemiological surveillance comprising a total of 2,301 patients, we identified a large outbreak caused by an Mtb strain of the Haarlem lineage. The main performance outcome measure of whole genome sequencing (WGS) analyses was the degree of correlation of the WGS analyses with contact tracing data and the spatio-temporal distribution of the outbreak cases. WGS analyses of the 86 isolates revealed 85 single nucleotide polymorphisms (SNPs), subdividing the outbreak into seven genome clusters (two to 24 isolates each), plus 36 unique SNP profiles. WGS results showed that the first outbreak isolates detected in 1997 were falsely clustered by classical genotyping. In 1998, one clone (termed “Hamburg clone”) started expanding, apparently independently from differences in the social environment of early cases. Genome-based clustering patterns were in better accordance with contact tracing data and the geographical distribution of the cases than clustering patterns based on classical genotyping. A maximum of three SNPs were identified in eight confirmed human-to-human transmission chains, involving 31 patients. We estimated the Mtb genome evolutionary rate at 0.4 mutations per genome per year. This rate suggests that Mtb grows in its natural host with a doubling time of approximately 22 h (400 generations per year). Based on the genome variation discovered, emergence of the Hamburg clone was dated back to a period between 1993 and 1997, hence shortly before the discovery of the outbreak through epidemiological surveillance.
Conclusions
Our findings suggest that WGS is superior to conventional genotyping for Mtb pathogen tracing and investigating micro-epidemics. WGS provides a measure of Mtb genome evolution over time in its natural host context.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Tuberculosis—a contagious bacterial disease that usually infects the lungs—is a major public health problem, particularly in low- and middle-income countries. In 2011, an estimated 8.7 million people developed tuberculosis globally, and 1.4 million people died from the disease. Tuberculosis is second only to HIV/AIDS in terms of global deaths from a single infectious agent. Mycobacterium tuberculosis, the bacterium that causes tuberculosis, is readily spread in airborne droplets when people with active disease cough or sneeze. The characteristic symptoms of tuberculosis include persistent cough, weight loss, fever, and night sweats. Diagnostic tests for the disease include sputum smear analysis (examination of mucus coughed up from the lungs for the presence of M. tuberculosis), mycobacterial culture (growth of M. tuberculosis from sputum), and chest X-rays. Tuberculosis can be cured by taking several antibiotics daily for at least six months, although the recent emergence of multidrug-resistant M. tuberculosis is making tuberculosis harder to treat.
Why Was This Study Done?
Although efforts to reduce the global burden of tuberculosis are showing some improvements, the annual decline in the number of people developing tuberculosis continues to be slow. To develop optimized control strategies, experts need to be able to accurately track M. tuberculosis transmission within human populations. Because M. tuberculosis, like all bacteria, accumulates genetic changes over time, there are many different strains (genetic variants) of M. tuberculosis. Genotyping methods have been developed that identify different bacterial strains by examining specific regions of the bacterial genome (blueprint), but because these methods examine only a small part of the genome, they may not distinguish between related transmission chains. That is, traditional strain genotyping methods may not be able to determine accurately where a tuberculosis outbreak started or how it spread through a population. In this longitudinal cohort study, the researchers compare the ability of whole genome sequencing (WGS), which is rapidly becoming widely available, and traditional genotyping to provide information about a recent German tuberculosis outbreak. In a longitudinal cohort study, a population is followed over time to analyze the occurrence of a specific disease.
What Did the Researchers Do and Find?
During long-term (1997–2010) population-based molecular epidemiological surveillance (disease surveillance that uses molecular techniques rather than reports of illness) in Hamburg and Schleswig-Holstein, the researchers identified a large tuberculosis outbreak caused by M. tuberculosis isolates of the Haarlem lineage using classical strain typing. The researchers examined each of the 86 isolates from this outbreak using WGS and classical genotyping and asked whether the results of these two approaches correlated with contact tracing data (information is routinely collected about the people a patient with tuberculosis has recently met so that these contacts can be tested for tuberculosis and treated if necessary) and with the spatio-temporal distribution of outbreak cases. WGS of the isolates identified 85 single nucleotide polymorphisms (SNPs; genomic sequence variants in which single building blocks, or nucleotides, are altered) that subdivided the outbreak into seven clusters of isolates and 36 unique isolates. The WGS results showed that the first isolates of the outbreak were incorrectly clustered by classical genotyping and that one strain—the “Hamburg clone”—started expanding in 1998. Notably, the genome-based clustering patterns were in better accordance with contact tracing data and with the geographical distribution of cases than clustering patterns based on classical genotyping, and they identified eight confirmed human-to-human transmission chains that involved 31 patients and a maximum of three SNPs. Finally, the researchers used their WGS results to estimate that the Hamburg clone emerged between 1993 and 1997, shortly before the discovery of the tuberculosis outbreak through epidemiological surveillance.
What Do These Findings Mean?
These findings show that WGS can be used to identify specific strains within large tuberculosis outbreaks more accurately than classical genotyping. They also provide new information about the evolution of M. tuberculosis during outbreaks and indicate how WGS data should be interpreted in future genome-based molecular epidemiology studies. WGS has the potential to improve the molecular epidemiological surveillance and control of tuberculosis and of other infectious diseases. Importantly, note the researchers, ongoing reductions in the cost of WGS, the increased availability of “bench top” genome sequencers, and bioinformatics developments should all accelerate the implementation of WGS as a standard method for the identification of transmission chains in infectious disease outbreaks.
Additional Information
Please access these websites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001387.
The World Health Organization provides information (in several languages) on all aspects of tuberculosis, including the Global Tuberculosis Report 2012
The Stop TB Partnership is working towards tuberculosis elimination; patient stories about tuberculosis are available (in English and Spanish)
The US Centers for Disease Control and Prevention has information about tuberculosis, including information on tuberculosis genotyping (some information in English and Spanish)
The US National Institute of Allergy and Infectious Diseases also has detailed information on all aspects of tuberculosis
The Tuberculosis Survival Project, which aims to raise awareness of tuberculosis and provide support for people with tuberculosis, provides personal stories about treatment for tuberculosis; the Tuberculosis Vaccine Initiative also provides personal stories about dealing with tuberculosis
MedlinePlus has links to further information about tuberculosis (in English and Spanish)
Wikipedia has a page on whole-genome sequencing (note: Wikipedia is a free online encyclopedia that anyone can edit; available in several languages)
doi:10.1371/journal.pmed.1001387
PMCID: PMC3570532  PMID: 23424287
15.  GStream: Improving SNP and CNV Coverage on Genome-Wide Association Studies 
PLoS ONE  2013;8(7):e68822.
We present GStream, a method that combines genome-wide SNP and CNV genotyping in the Illumina microarray platform with unprecedented accuracy. This new method outperforms previous well-established SNP genotyping software. More importantly, the CNV calling algorithm of GStream dramatically improves the results obtained by previous state-of-the-art methods and yields an accuracy that is close to that obtained by purely CNV-oriented technologies like Comparative Genomic Hybridization (CGH). We demonstrate the superior performance of GStream using microarray data generated from HapMap samples. Using the reference CNV calls generated by the 1000 Genomes Project (1KGP) and well-known studies on whole genome CNV characterization based either on CGH or genotyping microarray technologies, we show that GStream can increase the number of reliably detected variants up to 25% compared to previously developed methods. Furthermore, the increased genome coverage provided by GStream allows the discovery of CNVs in close linkage disequilibrium with SNPs, previously associated with disease risk in published Genome-Wide Association Studies (GWAS). These results could provide important insights into the biological mechanism underlying the detected disease risk association. With GStream, large-scale GWAS will not only benefit from the combined genotyping of SNPs and CNVs at an unprecedented accuracy, but will also take advantage of the computational efficiency of the method.
doi:10.1371/journal.pone.0068822
PMCID: PMC3700900  PMID: 23844243
16.  Whole genome amplification and real-time PCR in forensic casework 
BMC Genomics  2009;10:159.
Background
WGA (Whole Genome Amplification) in forensic genetics can eliminate the technical limitations arising from low amounts of genomic DNA (gDNA). However, it has not been used to date because any amplification bias generated may complicate the interpretation of results. Our aim in this paper was to assess the applicability of MDA to forensic SNP genotyping by performing a comparative analysis of genomic and amplified DNA samples. A 26-SNPs TaqMan panel specifically designed for low copy number (LCN) and/or severely degraded genomic DNA was typed on 100 genomic as well as amplified DNA samples.
Results
Aliquots containing 1, 0.1 and 0.01 ng each of 100 DNA samples were typed for a 26-SNPs panel. Similar aliquots of the same DNA samples underwent multiple displacement amplification (MDA) before being typed for the same panel. Genomic DNA samples showed 0% PCR failure rate for all three dilutions, whilst the PCR failure rate of the amplified DNA samples was 0% for the 1 ng and 0.1 ng dilutions and 0.077% for the 0.01 ng dilution. The genotyping results of both the amplified and genomic DNA samples were also compared with reference genotypes of the same samples obtained by direct sequencing. The genomic DNA samples showed genotype concordance rates of 100% for all three dilutions while the concordance rates of the amplified DNA samples were 100% for the 1 ng and 0.1 ng dilutions and 99.923% for the 0.01 ng dilution. Moreover, ten artificially-degraded DNA samples, which gave no results when analyzed by current forensic methods, were also amplified by MDA and genotyped with 100% concordance.
Conclusion
We investigated the suitability of MDA material for forensic SNP typing. Comparative analysis of amplified and genomic DNA samples showed that a large number of SNPs could be accurately typed starting from just 0.01 ng of template. We found that the MDA genotyping call and accuracy rates were only slightly lower than those for genomic DNA. Indeed, when 10 pg of input DNA was used in MDA, we obtained 99.923% concordance, indicating a genotyping error rate of 1/1299 (7.7 × 10-4). This is quite similar to the genotyping error rate of STRs used in current forensic analysis. Such efficiency and accuracy of SNP typing of amplified DNA suggest that MDA can also generate large amounts of genome-equivalent DNA from a minimal amount of input DNA. These results show for the first time that MDA material is suitable for SNP-based forensic protocols and in general when samples fail to give interpretable STR results.
doi:10.1186/1471-2164-10-159
PMCID: PMC2675535  PMID: 19366436
17.  Genotype determination for polymorphisms in linkage disequilibrium 
BMC Bioinformatics  2009;10:63.
Background
Genome-wide association studies with single nucleotide polymorphisms (SNPs) show great promise to identify genetic determinants of complex human traits. In current analyses, genotype calling and imputation of missing genotypes are usually considered as two separated tasks. The genotypes of SNPs are first determined one at a time from allele signal intensities. Then the missing genotypes, i.e., no-calls caused by not perfectly separated signal clouds, are imputed based on the linkage disequilibrium (LD) between multiple SNPs. Although many statistical methods have been developed to improve either genotype calling or imputation of missing genotypes, treating the two steps independently can lead to loss of genetic information.
Results
We propose a novel genotype calling framework. In this framework, we consider the signal intensities and underlying LD structure of SNPs simultaneously by estimating both cluster parameters and haplotype frequencies. As a result, our new method outperforms some existing algorithms in terms of both call rates and genotyping accuracy. Our studies also suggest that jointly analyzing multiple SNPs in LD provides more accurate estimation of haplotypes than haplotype reconstruction methods that only use called genotypes.
Conclusion
Our study demonstrates that jointly analyzing signal intensities and LD structure of multiple SNPs is a better way to determine genotypes and estimate LD parameters.
doi:10.1186/1471-2105-10-63
PMCID: PMC2753842  PMID: 19228433
18.  Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation 
PLoS Computational Biology  2012;8(7):e1002604.
High coverage whole genome sequencing provides near complete information about genetic variation. However, other technologies can be more efficient in some settings by (a) reducing redundant coverage within samples and (b) exploiting patterns of genetic variation across samples. To characterize as many samples as possible, many genetic studies therefore employ lower coverage sequencing or SNP array genotyping coupled to statistical imputation. To compare these approaches individually and in conjunction, we developed a statistical framework to estimate genotypes jointly from sequence reads, array intensities, and imputation. In European samples, we find similar sensitivity (89%) and specificity (99.6%) from imputation with either 1× sequencing or 1 M SNP arrays. Sensitivity is increased, particularly for low-frequency polymorphisms (), when low coverage sequence reads are added to dense genome-wide SNP arrays — the converse, however, is not true. At sites where sequence reads and array intensities produce different sample genotypes, joint analysis reduces genotype errors and identifies novel error modes. Our joint framework informs the use of next-generation sequencing in genome wide association studies and supports development of improved methods for genotype calling.
Author Summary
In this work we address a series of questions prompted by the rise of next-generation sequencing as a data collection strategy for genetic studies. How does low coverage sequencing compare to traditional microarray based genotyping? Do studies increase sensitivity by collecting both sequencing and array data? What can we learn about technology error modes based on analysis of SNPs for which sequence and array data disagree? To answer these questions, we developed a statistical framework to estimate genotypes from sequence reads, array intensities, and imputation. Through experiments with intensity and read data from the Hapmap and 1000 Genomes (1000 G) Projects, we show that 1 M SNP arrays used for genome wide association studies perform similarly to 1× sequencing. We find that adding low coverage sequence reads to dense array data significantly increases rare variant sensitivity, but adding dense array data to low coverage sequencing has only a small impact. Finally, we describe an improved SNP calling algorithm used in the 1000 G project, inspired by a novel next-generation sequencing error mode identified through analysis of disputed SNPs. These results inform the use of next-generation sequencing in genetic studies and model an approach to further improve genotype calling methods.
doi:10.1371/journal.pcbi.1002604
PMCID: PMC3395607  PMID: 22807667
19.  Methods of tagSNP selection and other variables affecting imputation accuracy in swine 
BMC Genetics  2013;14:8.
Background
Genotype imputation is a cost efficient alternative to use of high density genotypes for implementing genomic selection. The objective of this study was to investigate variables affecting imputation accuracy from low density tagSNP (average distance between tagSNP from 100kb to 1Mb) sets in swine, selected using LD information, physical location, or accuracy for genotype imputation. We compared results of imputation accuracy based on several sets of low density tagSNP of varying densities and selected using three different methods. In addition, we assessed the effect of varying size and composition of the reference panel of haplotypes used for imputation.
Results
TagSNP density of at least 1 tagSNP per 340kb (∼7000 tagSNP) selected using pairwise LD information was necessary to achieve average imputation accuracy higher than 0.95. A commercial low density (9K) tagSNP set for swine was developed concurrent to this study and an average accuracy of imputation of 0.951 based on these tagSNP was estimated. Construction of a haplotype reference panel was most efficient when these haplotypes were obtained from randomly sampled individuals. Increasing the size of the original reference haplotype panel (128 haplotypes sampled from 32 sire/dam/offspring trios phased in a previous study) led to an overall increase in imputation accuracy (IA = 0.97 with 512 haplotypes), but was especially useful in increasing imputation accuracy of SNP with MAF below 0.1 and for SNP located in the chromosomal extremes (within 5% of chromosome end).
Conclusion
The new commercially available 9K tagSNP set can be used to obtain imputed genotypes with high accuracy, even when imputation is based on a comparably small panel of reference haplotypes (128 haplotypes). Average imputation accuracy can be further increased by adding haplotypes to the reference panel. In addition, our results show that randomly sampling individuals to genotype for the construction of a reference haplotype panel is more cost efficient than specifically sampling older animals or trios with no observed loss in imputation accuracy. We expect that the use of imputed genotypes in swine breeding will yield highly accurate predictions of GEBV, based on the observed accuracy and reported results in dairy cattle, where genomic evaluation of some individuals is based on genotypes imputed with the same accuracy as our Yorkshire population.
doi:10.1186/1471-2156-14-8
PMCID: PMC3734000  PMID: 23433396
Genotype imputation; Pigs; Reference panel size
20.  KRLMM: an adaptive genotype calling method for common and low frequency variants 
BMC Bioinformatics  2014;15:158.
Background
SNP genotyping microarrays have revolutionized the study of complex disease. The current range of commercially available genotyping products contain extensive catalogues of low frequency and rare variants. Existing SNP calling algorithms have difficulty dealing with these low frequency variants, as the underlying models rely on each genotype having a reasonable number of observations to ensure accurate clustering.
Results
Here we develop KRLMM, a new method for converting raw intensities into genotype calls that aims to overcome this issue. Our method is unique in that it applies careful between sample normalization and allows a variable number of clusters k (1, 2 or 3) for each SNP, where k is predicted using the available data. We compare our method to four genotyping algorithms (GenCall, GenoSNP, Illuminus and OptiCall) on several Illumina data sets that include samples from the HapMap project where the true genotypes are known in advance. All methods were found to have high overall accuracy (> 98%), with KRLMM consistently amongst the best. At low minor allele frequency, the KRLMM, OptiCall and GenoSNP algorithms were observed to be consistently more accurate than GenCall and Illuminus on our test data.
Conclusions
Methods that tailor their approach to calling low frequency variants by either varying the number of clusters (KRLMM) or using information from other SNPs (OptiCall and GenoSNP) offer improved accuracy over methods that do not (GenCall and Illuminus). The KRLMM algorithm is implemented in the open-source crlmm package distributed via the Bioconductor project (http://www.bioconductor.org).
doi:10.1186/1471-2105-15-158
PMCID: PMC4064501  PMID: 24886250
Genotyping; Clustering; Microarray data analysis
21.  Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data 
BMC Genomics  2012;13:726.
Background
Next Generation Sequencing has provided comprehensive, affordable and high-throughput DNA sequences for Single Nucleotide Polymorphism (SNP) discovery in Acacia auriculiformis and Acacia mangium. Like other non-model species, SNP detection and genotyping in Acacia are challenging due to lack of genome sequences. The main objective of this study is to develop the first high-throughput SNP genotyping assay for linkage map construction of A. auriculiformis x A. mangium hybrids.
Results
We identified a total of 37,786 putative SNPs by aligning short read transcriptome data from four parents of two Acacia hybrid mapping populations using Bowtie against 7,839 de novo transcriptome contigs. Given a set of 10 validated SNPs from two lignin genes, our in silico SNP detection approach is highly accurate (100%) compared to the traditional in vitro approach (44%). Further validation of 96 SNPs using Illumina GoldenGate Assay gave an overall assay success rate of 89.6% and conversion rate of 37.5%. We explored possible factors lowering assay success rate by predicting exon-intron boundaries and paralogous genes of Acacia contigs using Medicago truncatula genome as reference. This assessment revealed that presence of exon-intron boundary is the main cause (50%) of assay failure. Subsequent SNPs filtering and improved assay design resulted in assay success and conversion rate of 92.4% and 57.4%, respectively based on 768 SNPs genotyping. Analysis of clustering patterns revealed that 27.6% of the assays were not reproducible and flanking sequence might play a role in determining cluster compression. In addition, we identified a total of 258 and 319 polymorphic SNPs in A. auriculiformis and A. mangium natural germplasms, respectively.
Conclusion
We have successfully discovered a large number of SNP markers in A. auriculiformis x A. mangium hybrids using next generation transcriptome sequencing. By using a reference genome from the most closely related species, we converted most SNPs to successful assays. We also demonstrated that Illumina GoldenGate genotyping together with manual clustering can provide high quality genotypes for a non-model species like Acacia. These SNPs markers are not only important for linkage map construction, but will be very useful for hybrid discrimination and genetic diversity assessment of natural germplasms in the future.
doi:10.1186/1471-2164-13-726
PMCID: PMC3556151  PMID: 23265623
22.  EM algorithm for Bayesian estimation of genomic breeding values 
BMC Genetics  2010;11:3.
Background
In genomic selection, a model for prediction of genome-wide breeding value (GBV) is constructed by estimating a large number of SNP effects that are included in a model. Two Bayesian methods based on MCMC algorithm, Bayesian shrinkage regression (BSR) method and stochastic search variable selection (SSVS) method, (which are called BayesA and BayesB, respectively, in some literatures), have been so far proposed for the estimation of SNP effects. However, much computational burden is imposed on the MCMC-based Bayesian methods. A method with both high computing efficiency and prediction accuracy is desired to be developed for practical use of genomic selection.
Results
EM algorithm applicable for BSR is described. Subsequently, we propose a new EM-based Bayesian method, called wBSR (weighted BSR), which is a modification of BSR incorporating a weight for each SNP according to the strength of its association to a trait. Simulation experiments show that the computational time is much reduced with wBSR based on EM algorithm and the accuracy in predicting GBV is improved by wBSR in comparison with BSR based on MCMC algorithm. However, the accuracy of predicted GBV with wBSR is inferior to that with SSVS based on MCMC algorithm which is currently considered to be a method of choice for genomic selection.
Conclusions
EM-based wBSR method proposed in this study is much advantageous over MCMC-based Bayesian methods in computational time and can predict GBV more accurately than MCMC-based BSR. Therefore, wBSR is considered a practical method for genomic selection with a large number of SNP markers.
doi:10.1186/1471-2156-11-3
PMCID: PMC2845064  PMID: 20092655
23.  Accuracy of Estimation of Genomic Breeding Values in Pigs Using Low-Density Genotypes and Imputation 
G3: Genes|Genomes|Genetics  2014;4(4):623-631.
Genomic selection has the potential to increase genetic progress. Genotype imputation of high-density single-nucleotide polymorphism (SNP) genotypes can improve the cost efficiency of genomic breeding value (GEBV) prediction for pig breeding. Consequently, the objectives of this work were to: (1) estimate accuracy of genomic evaluation and GEBV for three traits in a Yorkshire population and (2) quantify the loss of accuracy of genomic evaluation and GEBV when genotypes were imputed under two scenarios: a high-cost, high-accuracy scenario in which only selection candidates were imputed from a low-density platform and a low-cost, low-accuracy scenario in which all animals were imputed using a small reference panel of haplotypes. Phenotypes and genotypes obtained with the PorcineSNP60 BeadChip were available for 983 Yorkshire boars. Genotypes of selection candidates were masked and imputed using tagSNP in the GeneSeek Genomic Profiler (10K). Imputation was performed with BEAGLE using 128 or 1800 haplotypes as reference panels. GEBV were obtained through an animal-centric ridge regression model using de-regressed breeding values as response variables. Accuracy of genomic evaluation was estimated as the correlation between estimated breeding values and GEBV in a 10-fold cross validation design. Accuracy of genomic evaluation using observed genotypes was high for all traits (0.65−0.68). Using genotypes imputed from a large reference panel (accuracy: R2 = 0.95) for genomic evaluation did not significantly decrease accuracy, whereas a scenario with genotypes imputed from a small reference panel (R2 = 0.88) did show a significant decrease in accuracy. Genomic evaluation based on imputed genotypes in selection candidates can be implemented at a fraction of the cost of a genomic evaluation using observed genotypes and still yield virtually the same accuracy. On the other side, using a very small reference panel of haplotypes to impute training animals and candidates for selection results in lower accuracy of genomic evaluation.
doi:10.1534/g3.114.010504
PMCID: PMC4059235  PMID: 24531728
genomic selection; genotype imputation; swine; shared data resources; GenPred
24.  Single Nucleotide Polymorphism (SNP)-Strings: An Alternative Method for Assessing Genetic Associations 
PLoS ONE  2014;9(4):e90034.
Background
Genome-wide association studies (GWAS) identify disease-associations for single-nucleotide-polymorphisms (SNPs) from scattered genomic-locations. However, SNPs frequently reside on several different SNP-haplotypes, only some of which may be disease-associated. This circumstance lowers the observed odds-ratio for disease-association.
Methodology/Principal Findings
Here we develop a method to identify the two SNP-haplotypes, which combine to produce each person’s SNP-genotype over specified chromosomal segments. Two multiple sclerosis (MS)-associated genetic regions were modeled; DRB1 (a Class II molecule of the major histocompatibility complex) and MMEL1 (an endopeptidase that degrades both neuropeptides and β-amyloid). For each locus, we considered sets of eleven adjacent SNPs, surrounding the putative disease-associated gene and spanning ∼200 kb of DNA. The SNP-information was converted into an ordered-set of eleven-numbers (subject-vectors) based on whether a person had zero, one, or two copies of particular SNP-variant at each sequential SNP-location. SNP-strings were defined as those ordered-combinations of eleven-numbers (0 or 1), representing a haplotype, two of which combined to form the observed subject-vector. Subject-vectors were resolved using probabilistic methods. In both regions, only a small number of SNP-strings were present. We compared our method to the SHAPEIT-2 phasing-algorithm. When the SNP-information spanning 200 kb was used, SHAPEIT-2 was inaccurate. When the SHAPEIT-2 window was increased to 2,000 kb, the concordance between the two methods, in both of these eleven-SNP regions, was over 99%, suggesting that, in these regions, both methods were quite accurate. Nevertheless, correspondence was not uniformly high over the entire DNA-span but, rather, was characterized by alternating peaks and valleys of concordance. Moreover, in the valleys of poor-correspondence, SHAPEIT-2 was also inconsistent with itself, suggesting that the SNP-string method is more accurate across the entire region.
Conclusions/Significance
Accurate haplotype identification will enhance the detection of genetic-associations. The SNP-string method provides a simple means to accomplish this and can be extended to cover larger genomic regions, thereby improving a GWAS’s power, even for those published previously.
doi:10.1371/journal.pone.0090034
PMCID: PMC3984082  PMID: 24727690
25.  GACT: a Genome build and Allele definition Conversion Tool for SNP imputation and meta-analysis in genetic association studies 
BMC Genomics  2014;15:610.
Background
Genome-wide association studies (GWAS) have successfully identified genes associated with complex human diseases. Although much of the heritability remains unexplained, combining single nucleotide polymorphism (SNP) genotypes from multiple studies for meta-analysis will increase the statistical power to identify new disease-associated variants. Meta-analysis requires same allele definition (nomenclature) and genome build among individual studies. Similarly, imputation, commonly-used prior to meta-analysis, requires the same consistency. However, the genotypes from various GWAS are generated using different genotyping platforms, arrays or SNP-calling approaches, resulting in use of different genome builds and allele definitions. Incorrect assumptions of identical allele definition among combined GWAS lead to a large portion of discarded genotypes or incorrect association findings. There is no published tool that predicts and converts among all major allele definitions.
Results
In this study, we have developed a tool, GACT, which stands for Genome build and Allele definition Conversion Tool, that predicts and inter-converts between any of the common SNP allele definitions and between the major genome builds. In addition, we assessed several factors that may affect imputation quality, and our results indicated that inclusion of singletons in the reference had detrimental effects while ambiguous SNPs had no measurable effect. Unexpectedly, exclusion of genotypes with missing rate > 0.001 (40% of study SNPs) showed no significant decrease of imputation quality (even significantly higher when compared to the imputation with singletons in the reference), especially for rare SNPs.
Conclusion
GACT is a new, powerful, and user-friendly tool with both command-line and interactive online versions that can accurately predict, and convert between any of the common allele definitions and between genome builds for genome-wide meta-analysis and imputation of genotypes from SNP-arrays or deep-sequencing, particularly for data from the dbGaP and other public databases.
GACT software
http://www.uvm.edu/genomics/software/gact
doi:10.1186/1471-2164-15-610
PMCID: PMC4223508  PMID: 25038819
Allele definition (nomenclature); Genome build; Genome-wide association study (GWAS); Imputation; Meta-analysis

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