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1.  Harnessing genomics to identify environmental determinants of heritable disease 
Mutation research  2012;752(1):6-9.
Next-generation sequencing technologies can now be used to directly measure heritable de novo DNA sequence mutations in humans. However, these techniques have not been used to examine environmental factors that induce such mutations and their associated diseases. To address this issue, a working group on environmentally induced germline mutation analysis (ENIGMA) met in October 2011 to propose the necessary foundational studies, which include sequencing of parent–offspring trios from highly exposed human populations, and controlled dose–response experiments in animals. These studies will establish background levels of variability in germline mutation rates and identify environmental agents that influence these rates and heritable disease. Guidance for the types of exposures to examine come from rodent studies that have identified agents such as cancer chemotherapeutic drugs, ionizing radiation, cigarette smoke, and air pollution as germ-cell mutagens. Research is urgently needed to establish the health consequences of parental exposures on subsequent generations.
doi:10.1016/j.mrrev.2012.08.002
PMCID: PMC3556182  PMID: 22935230
Germ cell; Heritable mutation; Next generation sequencing; Copy number variants
2.  Congenital Anomalies in the Children of Cancer Survivors: A Report From the Childhood Cancer Survivor Study 
Journal of Clinical Oncology  2011;30(3):239-245.
Purpose
Children with cancer receive mutagenic treatments, which raises concern about the potential transmissibility of germline damage to their offspring. This question has been inadequately studied to date because of a lack of detailed individual treatment exposure assessment such as gonadal radiation doses.
Methods
Within the Childhood Cancer Survivor Study, we performed a retrospective cohort analysis of validated cases of congenital anomalies among 4,699 children of 1,128 male and 1,627 female childhood cancer survivors. We quantified chemotherapy with alkylating agents and radiotherapy doses to the testes and ovaries and related these exposures to risk of congenital anomalies using logistic regression.
Results
One hundred twenty-nine children had at least one anomaly (prevalence = 2.7%). For children whose mothers were exposed to radiation or alkylating agents versus neither, the prevalence of anomalies was 3.0% versus 3.5% (P = .51); corresponding figures were 1.9% versus 1.7% (P = .79) for the children of male survivors. Neither ovarian radiation dose (mean, 1.19 Gy; odds ratio [OR] = 0.59; 95% CI, 0.20 to 1.75 for 2.50+ Gy) nor testicular radiation dose (mean, 0.48 Gy; OR = 1.01; 95% CI, 0.36 to 2.83 for 0.50+ Gy) was related to risk of congenital anomalies. Treatment with alkylating agents also was not significantly associated with anomalies in the children of male or female survivors.
Conclusion
Our findings offer strong evidence that the children of cancer survivors are not at significantly increased risk for congenital anomalies stemming from their parent's exposure to mutagenic cancer treatments. This information is important for counseling cancer survivors planning to have children.
doi:10.1200/JCO.2011.37.2938
PMCID: PMC3269950  PMID: 22162566
3.  Trisomy 8: a common finding in mouse embryonic stem (ES) cell lines 
Background
Obtaining a germ cell line is one of the most important steps in developing a transgenic or knockout mouse with a targeted mutated gene of interest. A common problem with this technology is that embryonic stem (ES) cells often lack, or are extremely inefficient at, germ line transmission.
Results
To determine whether chromosomal anomalies are correlated with inefficient ES cell germ line transmission, we examined 97 constructed ES cell lines using conventional cytogenetic analysis, and fluorescence in situ hybridization (FISH). Chromosomal abnormalities occurred in 44 (45%) out of the 97 specimens analyzed: 31 specimens had trisomy 8 or mosaic trisomy 8, eight specimens had partial trisomy 8 resulting from unbalanced translocations, and five specimens had other chromosomal anomalies.
Conclusions
Our data suggest that chromosomal analysis is an important tool for improving the yield and quality of gene targeting experiments.
doi:10.1186/1755-8166-6-3
PMCID: PMC3564830  PMID: 23320952
Mouse ES cells; Chromosomal aberrations; FISH; Mosaicism
4.  Genetic Disease in the Children of Danish Survivors of Childhood and Adolescent Cancer 
Journal of Clinical Oncology  2011;30(1):27-33.
Purpose
Preconception radiation and chemotherapy have the potential to produce germ cell mutations leading to genetic disease in the next generation. Dose-response relationships were evaluated between cancer treatments and untoward pregnancy outcomes.
Patients and Methods
A case-cohort study was conducted involving 472 Danish survivors of childhood and adolescent cancer and their 1,037 pregnancies. Adverse outcomes included 159 congenital malformations, six chromosomal abnormalities, seven stillbirths, and nine neonatal deaths. Preconception radiation doses to the gonads, uterus, and pituitary gland and administered chemotherapy were quantified based on medical records and related to adverse outcomes using a generalized estimating equation model.
Results
No statistically significant associations were found between genetic disease in children and parental treatment with alkylating drugs or preconception radiation doses to the testes in male and ovaries in female cancer survivors. Specifically, the risk of genetic disease was similar among the children of irradiated survivors when compared with nonirradiated survivors (relative risk [RR], 1.02; 95% CI, 0.59 to 1.44; P = .94). A statistically significant association between abdomino-pelvic irradiation and malformations, stillbirths, and neonatal deaths was not seen in the children of female survivors overall (P = .07) or in the children of mothers receiving high uterine doses (mean, 13.5 Gy; max, 100 Gy; RR, 2.3; 95% CI, 0.95 to 5.56).
Conclusion
Mutagenic chemotherapy and radiotherapy doses to the gonads were not associated with genetic defects in children of cancer survivors. However, larger studies need to be conducted to further explore potential associations between high-dose pelvic irradiation and specific adverse pregnancy outcomes.
doi:10.1200/JCO.2011.35.0504
PMCID: PMC3255559  PMID: 22124106
5.  Development and Assessment of an Integrated Computer-Aided Detection Scheme for Digital Microscopic Images of Metaphase Chromosomes 
Journal of electronic imaging  2008;17(4):043008.
The authors developed an integrated computer-aided detection (CAD) scheme for detecting and classifying metaphase chromosomes as well as assessing its performance and robustness. This scheme includes an automatic metaphase-finding module and a karyotyping module and it was applied to a testing database with 200 digital microscopic images. The automatic metaphase-finding module detects analyzable metaphase cells using a feature-based artificial neural network (ANN). The ANN-generated outputs are analyzed by a receiver operating characteristics (ROC) method and an area under the ROC curve is 0.966. Then, the automatic karyotyping module classifies individual chromosomes of this cell into 24 types. In this module, a two-layer decision tree-based classifier with eight ANNs established in its connection nodes was optimized by a genetic algorithm. Chromosomes are first classified into seven groups by the ANN in the first layer. The chromosomes in these groups are then separately classified by seven ANNs into 24 types in the second layer. The classification accuracy is 94.5% in the first layer. Six ANNs achieved the accuracy above 95% and only one had lessened performance (80.6%) in the second layer. The overall classification accuracy is 91.5% as compared to 86.7% in the previous study using two independent datasets randomly acquired from our genetic laboratory. The results demonstrate that our automated scheme achieves high and robust performance in identification and classification of metaphase chromosomes.
doi:10.1117/1.3013459
PMCID: PMC3475421  PMID: 23087585
Metaphase chromosome; Karyotype; Computer-aided detection; Artificial neural network; Receiver operating characteristics
6.  Preconception exposure to mutagens: medical and other exposures to radiation and chemicals 
Journal of Community Genetics  2012;3(3):205-211.
Contrary to intuition, no environmental exposure has been proved to cause human germ line mutations that manifest as heritable disease in the offspring, not among the children born to survivors of the American atomic bombs in Japan nor in survivors of cancer in childhood, adolescence, or young adulthood who receive intensive chemotherapy, radiotherapy, or both. Even the smallest of recent case series had sufficient statistical power to exclude, with the usual assumptions, an increase as small as 20 % over baseline rates. One positive epidemiologic study of a localized epidemic of Down syndrome in Hungary found an association with periconceptual exposure to a pesticide used in fish farming, trichlorfon. Current population and occupational guidelines to protect against genetic effects of ionizing radiation should continue, with the understanding they are based on extrapolations from mouse experiments and mostly on males. Presently, pre-conceptual counseling for possible germ cell mutation due to the environment can be very reassuring, at least based on, in a sense, the worst-case exposures of cancer survivors. Prudence demands further study. Future work will address the issue with total genomic sequencing and epigenomic analysis.
doi:10.1007/s12687-012-0104-2
PMCID: PMC3419286  PMID: 22752838
Germ line mutations; Genetic counseling; Cancer survivors; Human environmental mutagens
7.  Hospitalizations among children of survivors of childhood and adolescent cancer: A population-based cohort study 
Curative but potentially mutagenic cancer therapy might lead to untoward disorders and increased hospitalization among the offspring of childhood cancer survivors. Hospitalizations in childhood were evaluated in a population-based cohort of 1,920 offspring of 3,963 childhood cancer survivors, 6,394 offspring of 5,657 siblings, and 9,594 population-based comparisons. The Danish Cancer Registry, Central Population Register, and National Hospital Register were used to identify study subjects and hospitalizations. The probability for children in the offspring cohorts of being hospitalized before a given age was estimated using the Kaplan-Meier method. Hospitalization rate ratios (HRRs) were calculated using a Cox proportional hazards model with population comparisons as referent. Little differences in hospitalization histories were seen among offspring in the three cohorts. HRRs of overall hospitalization was 1.05 (95% CI, 0.98–1.12) for offspring of survivors and 1.01 (95% CI, 0.97–1.05) for offspring of siblings, neither of which was significantly different from that of population comparisons. No significant associations were seen for most of the main diagnostic groups of diseases including infections and perinatal disorders. A six-fold excess risk of hospitalization for malignant tumors in survivors’ offspring, however, could largely be explained by hereditary cancer syndromes, and part of the 2-fold excess hospitalization for benign tumors might similarly be explained by an underlying genetic susceptibility or by increased surveillance of children born to survivors. Assuming that hospitalization is an indicator of multifactorial genetic disease, the findings provide further reassurance that cancer therapies do not confer a high risk of such conditions in offspring born after treatments.
doi:10.1002/ijc.25286
PMCID: PMC2958229  PMID: 21351267
cancer survivor; childhood cancer; germ-cell mutation; hospitalization in offspring
8.  Automated Analysis of Fluorescent in situ Hybridization (FISH) Labeled Genetic Biomarkers in Assisting Cervical Cancer Diagnosis 
The numerical and/or structural deviation of some chromosomes (i.e., monosomy and polysomy of chromosomes 3 and X) are routinely used as positive genetic biomarkers to diagnose cervical cancer and predict the disease progression. Among the available diagnostic methods to analyze the aneusomy of chromosomes 3 and X, fluorescence in situ hybridization (FISH) technology has demonstrated significant advantages in assisting clinicians to more accurately detect and diagnose cervical carcinoma at an early stage, in particular for the women at a high risk for progression of low-grade and high-grade squamous intra-epithelium lesions (LSIL and HSIL). In order to increase the diagnostic accuracy, consistency, and efficiency from that of manual FISH analysis, this study aims to develop and test an automated FISH analysis method that includes a two-stage scheme. In the first stage, an interactive multiple-threshold algorithm is utilized to segment potential interphase nuclei candidates distributed in different intensity levels and a rule-based classifier is implemented to identify analyzable interphase cells. In the second stage, FISH labeled biomarker spots of chromosomes 3 and X are segmented by a top-hat transform. The independent FISH spots are then detected by a knowledge-based classifier, which enables recognition of the splitting and stringy FISH signals. Finally, the ratio of abnormal interphase cells with numerical changes of chromosomes 3 and X is calculated to detect positive cases. The experimental results of four test cases showed high agreement of FISH analysis results between the automated scheme and the cytogeneticist’s analysis including 92.7% to 98.7% agreement in cell segmentation and 4.4% to 11.0% difference in cell classification. This preliminary study demonstrates that the feasibility of potentially applying the automatic FISH analysis method to expedite the screening and detecting cervical cancer at an early stage.
PMCID: PMC2916642  PMID: 20441233
Fluorescence in situ hybridization (FISH); Automated FISH analysis; Cervical cancer; Computer-aided detection (CAD); Chromosomes 3 and X
9.  PPARG and ADIPOQ gene polymorphisms increase type 2 diabetes risk in Asian Indian Sikhs: Pro12Ala still remains the strongest predictor 
We have examined the association of 14 tagging single nucleotide polymorphisms (tagSNPs) in peroxisome proliferator activated-receptor gamma transcripts 1 and 2 (PPARG1&2) and 5 tagSNPs in adiponectin (ADIPOQ) genes for their effect on type 2 diabetes (T2D) risk in Asian Indian Sikhs. A total of 554 T2D cases and 527 normoglycemic (NG) controls were examined for association with T2D and other sub-phenotypes of T2D. With the exception of a strong association of PPARG2/Pro12Ala with T2D [OR 0.13, 95%CI (0.03–0.56), p=0.0007], no other tagSNP in the PPARG locus revealed any significant association with T2D in this population. Similarly, none of the tagSNPs in the ADIPOQ gene was associated with T2D susceptibility in single-site analysis. However, haplotype analysis provided strong evidence of association of these loci with T2D. Three-site haplotype analysis in the PPARG locus using the two marginally associated SNPs (P/rs11715073 and P/rs3892175) in combination with Pro12 Ala (P/rs1801282) revealed a strong association of one ‘risk’ (CGC) (p=0.003; permutation p=0.015) and one ‘protective’ (CAC) (p =0.001; permutation p=0.005) haplotype associated with T2D. However, the major effect still appears to be driven by Pro12Ala as the association of these haplotypes did not remain significant when analyzed conditional upon Pro12Ala (p = 0.262). Additionally, two-site haplotype analysis in the ADIPOQ locus using only two marginally associated SNPs (AD/rs182052 and AD/rs7649121) revealed a significant protective association of the GA haplotype with T2D (p=0.009; permutation p=0.026). Multiple linear regression analysis also revealed significant association of an ADIPOQ variant (AD/rs12495941) with total body weight (p= 0.010), waist (p=0.024) and hip (p=0.021), although these associations were not significant after adjusting for multiple testing. Our new findings strongly suggest that the genetic variation in PPARG and ADIPOQ loci could contribute to risk for the development of T2D in Indian Sikhs. Identification of causal SNPs in these important biological and positional candidate genes would help determine true physiological significance of these loci in T2D and obesity.
doi:10.1016/j.metabol.2009.07.043
PMCID: PMC2843807  PMID: 19846176
10.  Risk of Cancer Among Children of Cancer Patients - A Nationwide Study in Finland 
Cancer treatments have the potential to cause germline mutations that might increase the risk of cancer in the offspring of former cancer patients. This risk was evaluated in a population-based study of early onset cancer patients in Finland.
Using nationwide registry data, 26,331 children of pediatric and early onset cancer patients (diagnosed under age 35 between 1953 and 2004) were compared to 58,155 children of siblings. Cancer occurrence among the children was determined by linkage with the cancer registry, and standardized incidence ratios (SIRs) were calculated comparing the observed number of cancers with that expected, based on rates in the general population of Finland.
Among the 9877 children born after their parent’s diagnosis, cancer risk was increased (SIR 1.67; 95% CI 1.29–2.12). However, after removing those with hereditary cancer syndromes, this increase disappeared (SIR 1.03; 95% CI 0.74–1.40). The overall risk of cancer among the offspring of siblings (SIR 1.07; 95% CI 0.94–1.21) was the same as among the offspring of the patients with non-hereditary cancer. Risk of cancer in offspring born prior to their parents cancer diagnosis was elevated (SIR 1.37, 95% CI 1.20–1.54), but removing hereditary syndromes resulted in a diminished and non-significant association (SIR 1.08, 95% CI 0.93–1.25).
This study shows that offspring of cancer patients are not at an increased risk of cancer except when the patient has a cancer-predisposing syndrome. These findings are directly relevant to counseling cancer survivors with regard to family planning.
doi:10.1002/ijc.24856
PMCID: PMC2801768  PMID: 19728329
Offspring; cancer survivors; genetic effects
11.  Variants in KCNQ1 increase type II diabetes susceptibility in South Asians: A study of 3,310 subjects from India and the US 
BMC Medical Genetics  2011;12:18.
Background
Polymorphisms in intron 15 of potassium voltage-gated channel, KQT-like subfamily member 1 (KCNQ1) gene have been associated with type II diabetes (T2D) in Japanese genome-wide association studies (GWAS). More recently a meta-analysis of European GWAS has detected a new independent signal associated with T2D in intron 11 of the KCNQ1 gene. The purpose of this investigation is to examine the role of these variants with T2D in populations of Asian Indian descent from India and the US.
Methods
We examined the association between four variants in the KCNQ1 gene with T2D and related quantitative traits in a total of 3,310 Asian Indian participants from two different cohorts comprising 2,431 individuals of the Punjabi case-control cohort from the Sikh Diabetes Study and 879 migrant Asian Indians living in the US.
Results
Our data confirmed the association of a new signal at the KCNQ1 locus (rs231362) with T2D showing an allelic odds ratio (OR) of 1.24 95%CI [1.08-1.43], p = 0.002 in the Punjabi cohort. A moderate association with T2D was also seen for rs2237895 in the Punjabi (OR 1.14; p = 0.036) and combined cohorts (meta-analysis OR 1.14; p = 0.018). Three-site haplotype analysis of rs231362, rs2237892, rs2237895 exhibited considerably stronger evidence of association of the GCC haplotype with T2D showing OR of 1.24 95%CI [1.00-1.53], p = 0.001, permutation p = 8 × 10-4 in combined cohorts. The 'C' risk allele carriers of rs2237895 had significantly reduced measures of HOMA-B in the US cohort (p = 0.008) as well as in combined cohort in meta-analysis (p = 0.009).
Conclusions
Our investigation has confirmed that the variation within the KCNQ1 locus confers a significant risk to T2D among Asian Indians. Haplotype analysis further suggested that the T2D risk associated with KCNQ1 SNPs may be derived from 'G' allele of rs231362 and 'C' allele of rs2237895 and this appears to be mediated through β cell function.
doi:10.1186/1471-2350-12-18
PMCID: PMC3037841  PMID: 21261977
12.  Stillbirth and neonatal death in relation to radiation exposure before conception: a retrospective cohort study 
Lancet  2010;376(9741):624-630.
Summary
Background
The reproductive implications of mutagenic treatments given to children with cancer are not clear. By studying the risk of untoward pregnancy outcomes, we indirectly assessed the risk of transmission of germline damage to the offspring of survivors of childhood cancer who were given radiotherapy and chemotherapy.
Methods
We did a retrospective cohort analysis, within the Childhood Cancer Survivor Study (CCSS), of the risk of stillbirth and neonatal death among the offspring of men and women who had survived childhood cancer. Patients in CCSS were younger than 21 years at initial diagnosis of an eligible cancer, were treated at 25 US institutions and one Canadian institution, and had survived for at least 5 years after diagnosis. We quantified the chemotherapy given to patients, and the preconception radiation doses to the testes, ovaries, uterus, and pituitary gland, and related these to the risk of stillbirth or neonatal death using Poisson regression analysis.
Findings
Among 1148 men and 1657 women who had survived childhood cancer, there were 4946 pregnancies. Irradiation of the testes (16 [1%] of 1270; adjusted relative risk 0·8 [95% CI 0·4–1·6]; mean dose 0·53 Gy [SD 1·40]) and pituitary gland (17 [3%] of 510, 1·1 [0·5–2·4] for more than 20·00 Gy; mean dose 10·20 Gy [13·0] for women), and chemotherapy with alkylating drugs (26 [2%] of 1195 women, 0·9 [0·5–1·5]; ten [1%] of 732 men, 1·2 [0·5–2·5]) were not associated with an increased risk of stillbirth or neonatal death. Uterine and ovarian irradiation significantly increased risk of stillbirth and neonatal death at doses greater than 10·00 Gy (five [18%] of 28, 9·1 [3·4–24·6]). For girls treated before menarche, irradiation of the uterus and ovaries at doses as low as 1·00–2·49 Gy significantly increased the risk of stillbirth or neonatal death (three [4%] of 69, 4·7 [1·2–19·0]).
Interpretation
Our findings do not support concern about heritable genetic changes affecting the risk of stillbirth and neonatal death in the offspring of men exposed to gonadal irradiation. However, uterine and ovarian irradiation had serious adverse effects on the offspring that were probably related to uterine damage. Careful management is warranted of pregnancies in women given high doses of pelvic irradiation before puberty.
doi:10.1016/S0140-6736(10)60752-0
PMCID: PMC3008402  PMID: 20655585
13.  The Childhood Cancer Survivor Study: A National Cancer Institute–Supported Resource for Outcome and Intervention Research 
Journal of Clinical Oncology  2009;27(14):2308-2318.
Survival for childhood cancer has increased dramatically over the last 40 years with 5-year survival rates now approaching 80%. For many diagnostic groups, rapid increases in survival began in the 1970s with the broader introduction of multimodality approaches, often including combination chemotherapy with or without radiation therapy. With this increase in rates of survivorship has come the recognition that survivors are at risk for adverse health and quality-of-life outcomes, with risk being influenced by host-, disease-, and treatment-related factors. In 1994, the US National Cancer Institute funded the Childhood Cancer Survivor Study, a multi-institutional research initiative designed to establish a large and extensively characterized cohort of more than 14,000 5-year survivors of childhood and adolescent cancer diagnosed between 1970 and 1986. This ongoing study, which reflects the single most comprehensive body of information ever assembled on childhood and adolescent cancer survivors, provides a dynamic framework and resource to investigate current and future questions about childhood cancer survivors.
doi:10.1200/JCO.2009.22.3339
PMCID: PMC2677920  PMID: 19364948
14.  Ovarian Failure and Reproductive Outcomes After Childhood Cancer Treatment: Results From the Childhood Cancer Survivor Study 
Journal of Clinical Oncology  2009;27(14):2374-2381.
These studies were undertaken to determine the effect, if any, of treatment for cancer diagnosed during childhood or adolescence on ovarian function and reproductive outcomes. We reviewed the frequency of acute ovarian failure, premature menopause, live birth, stillbirth, spontaneous and therapeutic abortion and birth defects in the participants in the Childhood Cancer Survivor Study (CCSS). Acute ovarian failure (AOF) occurred in 6.3% of eligible survivors. Exposure of the ovaries to high-dose radiation (especially over 10 Gy), alkylating agents and procarbazine, at older ages, were significant risk factors for AOF. Premature nonsurgical menopause (PM) occurred in 8% of participants versus 0.8% of siblings (rate ratio = 13.21; 95% CI, 3.26 to 53.51; P < .001). Risk factors for PM included attained age, exposure to increasing doses of radiation to the ovaries, increasing alkylating agent score, and a diagnosis of Hodgkin's lymphoma. One thousand two hundred twenty-seven male survivors reported they sired 2,323 pregnancies, and 1,915 female survivors reported 4,029 pregnancies. Offspring of women who received uterine radiation doses of more than 5 Gy were more likely to be small for gestational age (birthweight < 10 percentile for gestational age; 18.2% v 7.8%; odds ratio = 4.0; 95% CI, 1.6 to 9.8; P = .003). There were no differences in the proportion of offspring with simple malformations, cytogenetic syndromes, or single-gene defects. These studies demonstrated that women treated with pelvic irradiation and/or increasing alkylating agent doses were at risk for acute ovarian failure, premature menopause, and small-for-gestational-age offspring. There was no evidence for an increased risk of congenital malformations. Survivors should be generally reassured although some women have to consider their potentially shortened fertile life span in making educational and career choices.
doi:10.1200/JCO.2008.21.1839
PMCID: PMC2677923  PMID: 19364956
15.  Automated Classification of Metaphase Chromosomes: Optimization of an Adaptive Computerized Scheme 
We developed and tested a new automated chromosome karyotyping scheme using a two-layer classification platform. Our hypothesis is that by selecting most effective feature sets and adaptively optimizing classifiers for the different groups of chromosomes with similar image characteristics, we can reduce the complexity of automated karyotyping scheme and improve its performance and robustness. For this purpose, we assembled an image database involving 6900 chromosomes and implemented a genetic algorithm to optimize the topology of multi-feature based artificial neural networks (ANN). In the first layer of the scheme, a single ANN was employed to classify 24 chromosomes into seven classes. In the second layer, seven ANNs were adaptively optimized for seven classes to identify individual chromosomes. The scheme was optimized and evaluated using a “training-testing-validation” method. In the first layer, the classification accuracy for the validation dataset was 92.9%. In the second layer, classification accuracy of seven ANNs ranged from 67.5% to 97.5%, in which six ANNs achieved accuracy above 93.7% and only one had lessened performance. The maximum difference of classification accuracy between the testing and validation datasets is <1.7%. The study demonstrates that this new scheme achieves higher and robust performance in classifying chromosomes.
doi:10.1016/j.jbi.2008.05.004
PMCID: PMC2673199  PMID: 18585097
Artificial neural network; genetic algorithm; karyotype; metaphase chromosome; training-testing-validation
16.  Assessing Human Germ-Cell Mutagenesis in the Postgenome Era: A Celebration of the Legacy of William Lawson (Bill) Russell 
Birth defects, de novo genetic diseases, and chromosomal abnormality syndromes occur in ~5% of all live births, and affected children suffer from a broad range of lifelong health consequences. Despite the social and medical impact of these defects, and the 8 decades of research in animal systems that have identified numerous germ-cell mutagens, no human germ-cell mutagen has been confirmed to date. There is now a growing consensus that the inability to detect human germ-cell mutagens is due to technological limitations in the detection of random mutations rather than biological differences between animal and human susceptibility. A multidisciplinary workshop responding to this challenge convened at The Jackson Laboratory in Bar Harbor, Maine. The purpose of the workshop was to assess the applicability of an emerging repertoire of genomic technologies to studies of human germ-cell mutagenesis. Workshop participants recommended large-scale human germ-cell mutation studies be conducted using samples from donors with high-dose exposures, such as cancer survivors. Within this high-risk cohort, parents and children could be evaluated for heritable changes in (a) DNA sequence and chromosomal structure, (b) repeat sequences and minisatellites, and (c) global gene expression profiles and pathways. Participants also advocated the establishment of a bio-bank of human tissue samples from donors with well-characterized exposure, including medical and reproductive histories. This mutational resource could support large-scale, multiple-endpoint studies. Additional studies could involve the examination of transgenerational effects associated with changes in imprinting and methylation patterns, nucleotide repeats, and mitochondrial DNA mutations. The further development of animal models and the integration of these with human studies are necessary to provide molecular insights into the mechanisms of germ-cell mutations and to identify prevention strategies. Furthermore, scientific specialty groups should be convened to review and prioritize the evidence for germ-cell mutagenicity from common environmental, occupational, medical, and lifestyle exposures. Workshop attendees agreed on the need for a full-scale assault to address key fundamental questions in human germ-cell environmental mutagenesis. These include, but are not limited to, the following: Do human germ-cell mutagens exist? What are the risks to future generations? Are some parents at higher risk than others for acquiring and transmitting germ-cell mutations? Obtaining answers to these, and other critical questions, will require strong support from relevant funding agencies, in addition to the engagement of scientists outside the fields of genomics and germ-cell mutagenesis.
doi:10.1002/em.20284
PMCID: PMC2071946  PMID: 17295306
inherited disease; mutation detection; molecular genetic analysis; human genetic risk
17.  A clinical evaluation tool for SNP arrays, especially for autosomal recessive conditions in offspring of consanguineous parents 
Genetics in Medicine  2012;15(5):354-360.
Purpose:
This report describes a fast online tool to accelerate and improve clinical interpretation of single nucleotide polymorphism array results for diagnostic purposes, when consanguinity or inbreeding is identified.
Methods:
We developed a web-based program that permits entry of regions of homozygosity and, using OMIM, UCSC, and NCBI databases, retrieves genes within these regions as well as their associated autosomal recessive disorders. Relevant OMIM Clinical Synopses can be searched, using key clinical terms permitting further filtering for candidate genes and disorders.
Results:
The tool aids the clinician by arriving at a short list of relevant candidate disorders, guiding the continued diagnostic work-up. Its efficacy is illustrated by presenting seven patients who were diagnosed using this tool.
Conclusion:
The online single nucleotide polymorphism array evaluation tool rapidly and systematically identifies relevant genes and associated conditions mapping to identified regions of homozygosity. The built-in OMIM clinical feature search allows the user to further filter to reach a short list of candidate conditions relevant for the diagnosis, making it possible to strategize more focused diagnostic testing. The tabulated results can be downloaded and saved to the desktop in an Excel format. Its efficacy is illustrated by providing a few clinical examples.
doi:10.1038/gim.2012.136
PMCID: PMC3908554  PMID: 23100014
consanguinity; homozygosity; inbreeding; OMIM; SNP array
18.  De novo three-way chromosome translocation 46,XY,t(4;6;21)(p16;p21.1;q21) in a male with cleidocranial dysplasia 
Cleidocranial dysplasia (CCD) is an autosomal dominant skeletal dysplasia associated with cranial, clavicular, and dental anomalies. It is caused by mutations in the RUNX2 gene, which encodes an osteoblast-specific transcription factor and maps to chromosome 6p21. We report clinical and molecular cytogenetic studies in a patient with clinical features of CCD including wormian bones, delayed fontanel closure, hypoplastic clavicles and pubic rami, and supernumerary dentition. Additional abnormalities of bone growth and connective tissue, including easy bruisability, scarring, bleeding, joint hypermobility, and developmental delay were also observed. Molecular cytogenetic studies identified a de novo apparently balanced three-way translocation 46,XY,t(4;6;21)(p16;p21.1;q21). Further mapping revealed the breakpoint on 6p21 to be ∼50 kb upstream of exon 1 of the RUNX2 gene, with RUNX2 being intact on the derivative chromosome 6. We hypothesize that the proband's CCD has arisen from disruption of the developmentally regulated gene RUNX2 at the 6p21 breakpoint, due to a position effect mutation which may have altered the expression of the gene. Further studies might unravel a new regulatory element for RUNX2.
doi:10.1002/ajmg.a.31750
PMCID: PMC2663417  PMID: 18203189
three-way chromosome translocation; cleidocranial dysplasia (CCD); fluorescence in situ hybridization (FISH); phenotype–genotype correlation
19.  Impact of nine common type 2 diabetes risk polymorphisms in Asian Indian Sikhs: PPARG2 (Pro12Ala), IGF2BP2, TCF7L2 and FTO variants confer a significant risk 
BMC Medical Genetics  2008;9:59.
Background
Recent genome-wide association (GWA) studies have identified several unsuspected genes associated with type 2 diabetes (T2D) with previously unknown functions. In this investigation, we have examined the role of 9 most significant SNPs reported in GWA studies: [peroxisome proliferator-activated receptor gamma 2 (PPARG2; rs 1801282); insulin-like growth factor two binding protein 2 (IGF2BP2; rs 4402960); cyclin-dependent kinase 5, a regulatory subunit-associated protein1-like 1 (CDK5; rs7754840); a zinc transporter and member of solute carrier family 30 (SLC30A8; rs13266634); a variant found near cyclin-dependent kinase inhibitor 2A (CDKN2A; rs10811661); hematopoietically expressed homeobox (HHEX; rs 1111875); transcription factor-7-like 2 (TCF7L2; rs 10885409); potassium inwardly rectifying channel subfamily J member 11(KCNJ11; rs 5219); and fat mass obesity-associated gene (FTO; rs 9939609)].
Methods
We genotyped these SNPs in a case-control sample of 918 individuals consisting of 532 T2D cases and 386 normal glucose tolerant (NGT) subjects of an Asian Sikh community from North India. We tested the association between T2D and each SNP using unconditional logistic regression before and after adjusting for age, gender, and other covariates. We also examined the impact of these variants on body mass index (BMI), waist to hip ratio (WHR), fasting insulin, and glucose and lipid levels using multiple linear regression analysis.
Results
Four of the nine SNPs revealed a significant association with T2D; PPARG2 (Pro12Ala) [odds ratio (OR) 0.12; 95% confidence interval (CI) (0.03–0.52); p = 0.005], IGF2BP2 [OR 1.37; 95% CI (1.04–1.82); p = 0.027], TCF7L2 [OR 1.64; 95% CI (1.20–2.24); p = 0.001] and FTO [OR 1.46; 95% CI (1.11–1.93); p = 0.007] after adjusting for age, sex and BMI. Multiple linear regression analysis revealed significant association of two of nine investigated loci with diabetes-related quantitative traits. The 'C' (risk) allele of CDK5 (rs 7754840) was significantly associated with decreased HDL-cholesterol levels in both NGT (p = 0.005) and combined (NGT and T2D) (0.005) groups. The less common 'C' (risk) allele of TCF7L2 (rs 10885409) was associated with increased LDL-cholesterol (p = 0.010) in NGT and total and LDL-cholesterol levels (p = 0.008; p = 0.003, respectively) in combined cohort.
Conclusion
To our knowledge, this is first study reporting the role of some recently emerged loci with T2D in a high risk population of Asian Indian origin. Further investigations are warranted to understand the pathway-based functional implications of these important loci in T2D pathophysiology in different ethnicities.
doi:10.1186/1471-2350-9-59
PMCID: PMC2481250  PMID: 18598350

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