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1.  Validation of My Family Health Portrait for Six Common Heritable Conditions 
Genetics in Medicine  2010;12(6):370-375.
To assess the ability of My Family Health Portrait (MFHP) to accurately collect family history for six common heritable disorders.
Family history is useful to assess disease risk, but is not widely used. We compared the pedigree from MFHP, an online tool for collection of family history, to a pedigree supplemented by a genetics professional.
150 volunteers collected their family histories using MFHP. A genetic counselor interviewed the volunteers to validate the entries and add diagnoses, as needed. The content and the affection assignments of the pedigrees were compared. The pedigrees were entered into Family Healthware™ to assess risks for the diseases.
The sensitivity of MFHP varied among the 6 diseases (67–100%) compared to the supplemented pedigree. The specificities ranged from 92–100%. When the pedigrees were used to generate risk scores, MFHP yielded identical risks to the supplemented pedigree for 94–99% of the volunteers for diabetes and colon, breast, and ovarian cancer. The agreement was lower for coronary artery disease (68%) and stroke (83%).
These data support the validity of MFHP pedigrees for four common conditions – diabetes and colon, breast, and ovarian cancer. The tool performed less well for coronary artery disease and stroke. We recommend that the tool be improved to better capture information for these two common conditions.
PMCID: PMC3258571  PMID: 20479646
My Family Health Portrait; common disease; family history; risk assessment; pedigree
2.  Browsing Isolated Population Data 
BMC Bioinformatics  2005;6(Suppl 4):S17.
In our studies of genetically isolated populations in a remote mountain area in the center of Sardinia (Italy), we found that 80–85% of the inhabitants of each village belong to a single huge pedigree with families strictly connected to each other through hundreds of loops. Moreover, intermarriages between villages join pedigrees of different villages through links that make family trees even more complicated. Unfortunately, none of the commonly used pedigree drawing tools are able to draw the complete pedigree, whereas it is commonly accepted that the visual representation of families is very important as it helps researchers in identifying clusters of inherited traits and genotypes. We had a representation issue that compels researchers to work with subsets extracted from the overall genealogy, causing a serious loss of information on familiar relationships.
To visually explore such complex pedigrees, we developed PedNavigator, a browser for genealogical databases properly suited for genetic studies.
The PedNavigator is useful for genealogical research due to its capacity to represent family relations between persons and to make a visual verification of the links during family history reconstruction. As for genetic studies, it is helpful to follow propagation of a specific set of genetic markers (haplotype), or to select people for linkage analysis, showing relations between various branch of a family tree of affected subjects.
PedNavigator is an application integrated into a Framework designed to handle data for human genetic studies based on the Oracle platform. To allow the use of PedNavigator also to people not owning the same required informatics infrastructure or systems, we developed PedNavigator Lite with mainly the same features of the integrated one, based on MySQL database server. This version is free for academic users, and it is available for download from our site
PMCID: PMC1866391  PMID: 16351743
3.  Redesign of Pedigree Displays through User-centered Visualization 
A complete family history is critical to the assessment of genetic risk of hereditary diseases. Kinsys© is a family history-tracking program used by genetic counselors and healthcare professionals for risk assessment. A pedigree, which is a graphic drawing of family history, is the most important component in such a program. In this project, we analyzed the current pedigree displays of Kinsys© and identified their problems and limitations; and we developed innovative pedigree displays by principles of user-centered visualization methodology for a new version of Kinsys© that overcome some limitations of the original displays.
PMCID: PMC2244530
4.  Genealogical data in population medical genetics: Field guidelines 
Genetics and Molecular Biology  2013;37(1 Suppl):171-185.
This is a guide for fieldwork in Population Medical Genetics research projects. Data collection, handling, and analysis from large pedigrees require the use of specific tools and methods not widely familiar to human geneticists, unfortunately leading to ineffective graphic pedigrees. Initially, the objective of the pedigree must be decided, and the available information sources need to be identified and validated. Data collection and recording by the tabulated method is advocated, and the involved techniques are presented. Genealogical and personal information are the two main components of pedigree data. While the latter is unique to each investigation project, the former is solely represented by gametic links between persons. The triad of a given pedigree member and its two parents constitutes the building unit of a genealogy. Likewise, three ID numbers representing those three elements of the triad is the record field required for any pedigree analysis. Pedigree construction, as well as pedigree and population data analysis, varies according to the pre-established objectives, the existing information, and the available resources.
PMCID: PMC3983591  PMID: 24764752
medical genetics; population medical genetics; geographic clusters; isolates; rare diseases
5.  Generation of pedigree diagrams for web display using scalable vector graphics from a clinical trials database. 
The standard method of studying inherited disease is to observe its pattern of distribution in families, that is, its pattern in a pedigree. For clinical studies focused on inherited disease, a pedigree diagram is a valuable visual tool for the display of inheritance patterns. We describe the creation of a web-based pedigree display module for Trial/DB, a Web accessible database developed at the Yale Center for Medical Informatics (YCMI) to support clinical research studies. The pedigree diagram is generated dynamically from the database. The icons representing each subject in the pedigree are selectable hyperlinks that will display detailed clinical data collected on the subject. Microsoft Active Server Page and Scalable Vector Graphics (SVG) are used to create the interactive pedigree diagrams.
PMCID: PMC2243683  PMID: 11825175
6.  The family medical history as a tool in preconception consultation 
Journal of Community Genetics  2012;3(3):175-183.
A multigenerational medical family history graphically recorded as a pedigree or family tree is a cost-effective tool in preconception counseling to identify couples at risk to have offspring with inherited disorders and to identify if either partner has a personal risk for a disorder with a genetic etiology. Interpretation of a medical family history can provide risk assessment for reproductive planning and choices, inform a diagnosis to help identify a patient’s medical screening needs and clinical management, and build rapport with the patient or couple. The use of standardized pedigree nomenclature is paramount to healthcare delivery as electronic medical records become universal. The trend towards having patients prepare a medical family history in advance of the first clinic visit is a way to empower patients to take charge of their health, and also allow health professionals to spend more focused time in confirming and interpreting family history at the visit instead of constructing family history. This article reviews standardized pedigree symbols, clues to identifying “red flags” in family history (with a focus on preconception genetic counseling), the pedigree as a psychosocial tool, and resources for obtaining a medical family history.
PMCID: PMC3419295  PMID: 22810887
Electronic medical record; Family history; Genetic counseling; Pedigree; Standardized pedigree nomenclature
7.  Development and Validation of Pedigree Classification Criteria for Frontotemporal Lobar Degeneration 
JAMA neurology  2013;70(11):1411-1417.
A significant portion of frontotemporal lobar degeneration (FTLD) is due to inherited gene mutations, and we are unaware of a large sequential series that includes a recently discovered inherited cause of FTLD. There is also great need to develop clinical tools and approaches that will assist clinicians in the identification and counseling of patients with FTLD and their families regarding the likelihood of an identifiable genetic cause.
To ascertain the frequency of inherited FTLD and develop validated pedigree classification criteria for FTLD that provide a standardized means to evaluate pedigree information and insight into the likelihood of mutation-positive genetic test results for C9orf72, MAPT, and GRN.
Information about pedigrees and DNA was collected from 306 serially assessed patients with a clinical diagnosis of FTLD. This information included gene test results for C9orf72, MAPT, and GRN. Pedigree classification criteria were developed based on a literature review of FTLD genetics and pedigree tools and then refined by reviewing mutation-positive and -negative pedigrees to determine differentiating characteristics.
Academic medical center.
Patients with FTLD.
Familial risk.
The rate of C9orf72, MAPT, or GRN mutation–positive FTLD in this series was 15.4%. Categories designating the risk level for hereditary cause were termed high, medium, low, apparent sporadic, and unknown significance. Thirty-nine pedigrees (12.7%)met criteria for high, 31 (10.1%) for medium, 46 (15.0%) for low, 91 (29.7%) for apparent sporadic, and 99 (32.4%) for unknown significance. The mutation-detection rates were as follows: high, 64.1%; medium, 29%; low, 10.9%; apparent sporadic, 1.1%; and unknown significance, 7.1%. Mutation-detection rates differed significantly between the high and other categories.
Mutation rates are high in FTLD spectrum disorders, and the proposed criteria provide a validated standard for the classification of FTLD pedigrees. The combination of pedigree criteria and mutation-detection rates has important implications for genetic counseling and testing in clinical settings.
PMCID: PMC3906581  PMID: 24081456
8.  PedWiz: a web-based tool for pedigree informatics 
Frontiers in Genetics  2013;4:189.
A novel web-based tool PedWiz that pipelines the informatics process for pedigree data is introduced. PedWiz is designed to assist researchers in the analysis of pedigree data. It provides a convenient tool for pedigree informatics: descriptive statistics, relative pairs, genetic similarity coefficients, the variance-covariance matrix for three estimated coefficients of allele identical-by-descent sharing as well as mean allele sharing, a plot of the pedigree structures, and a visualization of the identity coefficients. With a renewed interest in linkage and other family based methods, PedWiz will be a valuable tool for the analysis of family data.
PMCID: PMC3782697  PMID: 24093024
pedigree; informatics; genetic similarity; identity-by-descent; relative pairs; family data
9.  VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees 
BMC Bioinformatics  2012;13(Suppl 8):S5.
Pedigree genotype datasets are used for analysing genetic inheritance and to map genetic markers and traits. Such datasets consist of hundreds of related animals genotyped for thousands of genetic markers and invariably contain multiple errors in both the pedigree structure and in the associated individual genotype data. These errors manifest as apparent inheritance inconsistencies in the pedigree, and invalidate analyses of marker inheritance patterns across the dataset. Cleaning raw datasets of bad data points (incorrect pedigree relationships, unreliable marker assays, suspect samples, bad genotype results etc.) requires expert exploration of the patterns of exposed inconsistencies in the context of the inheritance pedigree. In order to assist this process we are developing VIPER (Visual Pedigree Explorer), a software tool that integrates an inheritance-checking algorithm with a novel space-efficient pedigree visualisation, so that reported inheritance inconsistencies are overlaid on an interactive, navigable representation of the pedigree structure.
Methods and results
This paper describes an evaluation of how VIPER displays the different scales and types of dataset that occur experimentally, with a description of how VIPER's display interface and functionality meet the challenges presented by such data. We examine a range of possible error types found in real and simulated pedigree genotype datasets, demonstrating how these errors are exposed and explored using the VIPER interface and we evaluate the utility and usability of the interface to the domain expert.
Evaluation was performed as a two stage process with the assistance of domain experts (geneticists). The initial evaluation drove the iterative implementation of further features in the software prototype, as required by the users, prior to a final functional evaluation of the pedigree display for exploring the various error types, data scales and structures.
The VIPER display was shown to effectively expose the range of errors found in experimental genotyped pedigrees, allowing users to explore the underlying causes of reported inheritance inconsistencies. This interface will provide the basis for a full data cleaning tool that will allow the user to remove isolated bad data points, and reversibly test the effect of removing suspect genotypes and pedigree relationships.
PMCID: PMC3355332  PMID: 22607476
10.  Computer support for interpreting family histories of breast and ovarian cancer in primary care: comparative study with simulated cases 
BMJ : British Medical Journal  2000;321(7252):28-32.
To evaluate the potential effect of computer support on general practitioners' management of familial breast and ovarian cancer, and to compare the effectiveness of two different types of computer program.
Crossover experiment with balanced block design.
Of a random sample of 100 general practitioners from Buckinghamshire who were invited, 41 agreed to participate. From these, 36 were selected for a fully balanced study.
Doctors managed 18 simulated cases: 6 with computerised decision support system Risk Assessment in Genetics (RAGs), 6 with Cyrillic (an established pedigree drawing program designed for clinical geneticists), and 6 with pen and paper.
Main outcome measures
Number of appropriate management decisions made (maximum 6), mean time taken to reach a decision, number of pedigrees accurately drawn (maximum 6). Secondary measures were method of support preferred for particular aspects of managing family histories of cancer; importance of specific information on cancer genetics that might be provided by an “ideal computer program.”
RAGs resulted in significantly more appropriate management decisions (median 6) than either Cyrillic (median 3) or pen and paper (median 3); median difference between RAGs and Cyrillic 2.5 (95% confidence interval 2.0 to 3.0; P<0.0001). RAGs also resulted in significantly more accurate pedigrees (median 5) than both Cyrillic (median 3.5) and pen and paper (median 2); median difference between RAGs and Cyrillic 1.5 (1.0 to 2.0; P<0.0001). The time taken to use RAGs (median 178 seconds) was 51 seconds longer per case (95% confidence interval 36 to 65; P<0.0001) than pen and paper (median 124 seconds) but was less than Cyrillic (median 203 seconds; difference 23. (5 to 43; P=0.02)). 33 doctors (92% (78% to 98%)) preferred using RAGs overall. The most important elements of an “ideal computer program” for genetic advice in primary care were referral advice, the capacity to create pedigrees, and provision of evidence and explanations to support advice.
RAGs could enable general practitioners to be more effective gatekeepers to genetics services, empowering them to reassure the majority of patients with a family history of breast and ovarian cancer who are not at increased genetic risk.
PMCID: PMC27423  PMID: 10875832
11.  The role of large pedigrees in an era of high-throughput sequencing 
Human genetics  2012;131(10):1555-1563.
Rare variation is the current frontier in human genetics. The large pedigree design is practical, efficient, and well-suited for investigating rare variation. In large pedigrees, specific rare variants that co-segregate with a trait will occur in sufficient numbers so that effects can be measured, and evidence for association can be evaluated, by making use of methods that fully use the pedigree information. Evidence from linkage analysis can focus investigation, both reducing the multiple testing burden and expanding the variants that can be evaluated and followed up, as recent studies have shown. The large pedigree design requires only a small fraction of the sample size needed to identify rare variants of interest in population-based designs, and many highly suitable, well-understood, and available statistical and computational tools already exist. Samples consisting of large pedigrees with existing rich phenotype and genome scan data should be prime candidates for high-throughput sequencing in the search of the determinants of complex traits.
PMCID: PMC3638020  PMID: 22714655
12.  HC Forum®: a web site based on an international human cytogenetic database 
Nucleic Acids Research  2001;29(1):305-307.
Familial structural rearrangements of chromosomes represent a factor of malformation risk that could vary over a large range, making genetic counseling difficult. However, they also represent a powerful tool for increasing knowledge of the genome, particularly by studying breakpoints and viable imbalances of the genome. We have developed a collaborative database that now includes data on more than 4100 families, from which we have developed a web site called HC Forum® ( It offers geneticists assistance in diagnosis and in genetic counseling by assessing the malformation risk with statistical models. For researchers, interactive interfaces exhibit the distribution of chromosomal breakpoints and of the genome regions observed at birth in trisomy or in monosomy. Dedicated tools including an interactive pedigree allow electronic submission of data, which will be anonymously shown in a forum for discussions. After validation, data are definitively registered in the database with the email of the sender, allowing direct location of biological material. Thus HC Forum® constitutes a link between diagnosis laboratories and genome research centers, and after 1 year, more than 700 users from about 40 different countries already exist.
PMCID: PMC29821  PMID: 11125121
13.  A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees 
Bioinformatics  2012;29(2):197-205.
Motivation: The use of dense single nucleotide polymorphism (SNP) data in genetic linkage analysis of large pedigrees is impeded by significant technical, methodological and computational challenges. Here we describe Superlink-Online SNP, a new powerful online system that streamlines the linkage analysis of SNP data. It features a fully integrated flexible processing workflow comprising both well-known and novel data analysis tools, including SNP clustering, erroneous data filtering, exact and approximate LOD calculations and maximum-likelihood haplotyping. The system draws its power from thousands of CPUs, performing data analysis tasks orders of magnitude faster than a single computer. By providing an intuitive interface to sophisticated state-of-the-art analysis tools coupled with high computing capacity, Superlink-Online SNP helps geneticists unleash the potential of SNP data for detecting disease genes.
Results: Computations performed by Superlink-Online SNP are automatically parallelized using novel paradigms, and executed on unlimited number of private or public CPUs. One novel service is large-scale approximate Markov Chain–Monte Carlo (MCMC) analysis. The accuracy of the results is reliably estimated by running the same computation on multiple CPUs and evaluating the Gelman–Rubin Score to set aside unreliable results. Another service within the workflow is a novel parallelized exact algorithm for inferring maximum-likelihood haplotyping. The reported system enables genetic analyses that were previously infeasible. We demonstrate the system capabilities through a study of a large complex pedigree affected with metabolic syndrome.
Availability: Superlink-Online SNP is freely available for researchers at The system source code can also be downloaded from the system website.
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC3546794  PMID: 23162081
14.  RISK-XLR: A Microcomputer-Based Genetic Risk Program for X-Linked Recessive Traits 
A computer program, RISK-XLR, which calculates genetic risk for carrier status of a Mendelian X-linked recessive condition has been written for the Macintosh series of microcomputers. The program, which incorporates family information (number of normal sons, daughters and granddaughters with normal sons, etc.), mutation rate, fitness and carrier test results in the assessment of genetic risk, utilizes Bayesian conditional probability. “User-friendly” and “error trapping” features have been incorporated to minimize errors in data entry and to minimize training time. Family and laboratory data can be stored for future reference, modification(s) and recalculation(s). Hard-copy output is available for inclusion in counseling letters and/or patient charts. The program can handle large pedigrees containing up to 10 women whose genotype is unknown. Hemophilia and Duchenne muscular dystrophy specialty clinics may especially benefit from these programs. Educators involved in the teaching of genetic risk assessment may find the program useful in posing “what it” situations for solution by students.
PMCID: PMC2245119
15.  Genetic Counseling for Isolated GnRH Deficiency 
Molecular and cellular endocrinology  2011;346(1-2):102-109.
As our understanding of the complexities of the various etiologies and complex genetic architecture of GnRH deficiency grows, so too does the need to apply newly-developed genetic tools in a way that: a) is meaningful to individuals and their families; b) integrates all of the phenotypic features of this syndrome into a rationale; and c) provides up-to-date diagnostic technologies in a cost-effective algorithm of genetic testing. Genetic counseling aims to accomplish these goals through ascertainment of detailed family histories, targeted comprehensive phenotypic evaluations, informed selection of genetic testing, interpretation of genetic test results, and the provision of highly specific risk assessments and psychological support to individuals diagnosed with this reproductive condition.
This chapter offers a guide to incorporating this rapidly evolving state of knowledge of the pedigree and phenotypes into the process of selecting and prioritizing genetic testing. In addition, the provision of risk assessment that accounts for nuanced genetic concepts such as variable expressivity, incomplete penetrance, and oligogenicity, all of which are emerging features of the genetics of this clinical syndrome, is considered. Beyond translating genetic information, genetic counseling should address the psychological impact of embarrassment, shame, anxiety, and guilt that are often seen among individuals with reproductive disorders.
PMCID: PMC3185214  PMID: 21664415
genetic counseling; GnRH deficiency; Kallmann syndrome
16.  Two Search Techniques within a Human Pedigree Database 
This paper presents the basic features of two search techniques from MEGADATS-2 (MEdical Genetics Acquisition and DAta Transfer System), a system for collecting, storing, retrieving and plotting human family pedigrees. The individual search provides a quick method for locating an individual in the pedigree database. This search uses a modified soundex coding and an inverted file structure based on a composite key. The navigational search uses a set of pedigree traversal operations (individual, parent, mate, offspring, and sibling) and conventional Boolean logic to extract information from a pedigree database.
PMCID: PMC2580200
17.  Pedimap: Software for the Visualization of Genetic and Phenotypic Data in Pedigrees 
Journal of Heredity  2012;103(6):903-907.
Pedimap is a user-friendly software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees. Genetic data can include marker scores, Identity-by-Descent probabilities, and marker linkage map positions, allowing the visualization of haplotypes through lineages. The pedigrees can accommodate all types of inheritance, including selfing, cloning, and repeated backcrossing, and all ploidy levels are supported. Visual association of the genetic data with phenotypic data simplifies the exploration of large data sets, thereby improving breeding decision making. Data are imported from text files; in addition data exchange with other software packages (FlexQTLTM and GenomeStudioTM) is possible. Instructions for use and an executable version compatible with the Windows platform are available for free from
PMCID: PMC3510005  PMID: 23087384
genetic data; pedigree software; phenotypic data; plant breeding
18.  Veterans’ experience in using the online Surgeon General’s family health history tool 
Personalized medicine  2011;8(5):523-532.
To assess veterans’ experience and satisfaction in using the Surgeon General’s (SG) online family health history (FHH) tool, and determine the perceived facilitators and barriers to using the online SG-FHH tool.
Materials & methods
A mixed-method using both qualitative and quantitative approaches was employed in this study. A total of 35 veterans at the VA Medical Center in San Antonio, Texas, USA were invited to enter their FHH information using the online SG-FHH tool, complete the study’s satisfaction survey and participate in a short semi-structured interview. The goal of the semi-structured interviews was to assess participants perceived facilitators and barriers to using the online SG-FHH tool. All participants were also provided with a printed copy of their pedigree, which was generated by the SG-FHH tool and were encouraged to share it with their relatives and providers.
The majority of participants (91%) said that they had access to a computer with internet capability and 77% reported that they knew how to use a computer. More than two-thirds of the participants felt that items on the SG-FHH tool were easy to read and felt that FHH categories were relevant to their family’s health. Approximately 94% of participants viewed the SG-FHH tool as useful, and the majority of participants (97%) indicated that they were likely to recommend the tool to others. Content analysis of the semi-structured interviews highlighted several barriers to veterans’ use of the SG-FHH tool and their FHH information. These included: lack of patients’ knowledge regarding their relatives’ FHH, and privacy and confidentiality concerns.
This study provides information on the performance and functionality of an inexpensive and widely accessible method for FHH collection. Furthermore, our findings highlight several opportunities and challenges facing the utilization of FHH information as a clinical and genomic tool at the Veterans Health Administration (VHA). The results suggest that strategies that improve veterans’ knowledge regarding the importance of their FHH information and that address their concerns about privacy and confidentiality may enhance the successful implementation of FHH information into VHA clinical practice.
identifying a locally accepted method for FHH collection and documentation which can be conducted outside of the patient visit will reduce time burdens for providers and patients and allow for a focus on other important topics during clinic visits. Improvement in familial risk screening and assessment will enable the VHA to be prepared for personalized medicine and focus their resources on promoting critically important health behaviors for populations with the highest risk of developing chronic diseases and their complications.
PMCID: PMC3210025  PMID: 22076122
family health history; genomic services; Surgeon General’s online tool
19.  Proband Race/Ethnicity Affects Pedigree Completion Rate in a Genetic Study of Ischemic Stroke 
A recent meta-analysis suggested that racial/ethnic status is not a major determinant of willingness to participate in observational studies or treatment trials.However, little is known about the predictors of enrollment in family-based observational genetic studies. We tested the hypothesis that proband race/ethnicity is a significant predictor of enrolling a pedigree.
Univariable and multivariable logistic regression modeling was used to determine proband characteristics that predict DNA donation from both members of an affected sibling pair. A total of 619 adult male and female probands with first-time or recurrent ischemic stroke and a positive sibling history of stroke enrolled across 53 hospitals and clinics in the United States and Canada into the Siblings with Ischemic Stroke Study, a family based prospective genomics study.
In univariable analysis, probands with siblings who agreed to a blood draw for DNA analyses were more likely to be male and less likely to be nonwhite. In multivariable analysis, only race/ethnicity was significantly associated with likelihood of a proband’s having a sibling who agreed to a blood draw.
Contrary to observational studies that are not family based, the willingness of family members to participate in observational genetics studies may be influenced by race/ethnicity. This result reinforces the need for improving methods for recruiting diverse populations into genetic studies of stroke.
PMCID: PMC2715997  PMID: 18755410
Ethnicity; genetics; pedigree research; race; siblings; stroke
20.  The study of gene GJB2/DFNB1 causing deafness in humans by linkage analysis from district Peshawar 
Indian Journal of Human Genetics  2012;18(2):217-221.
Families with at least 2 or more individuals having hereditary hearing loss were enrolled from different areas of Khyber Pakhtoonkhwa, mainly from district Peshawar. Detailed history was taken from each family to minimize the presence of other abnormalities and environmental causes for deafness. Families were questioned about skin pigmentation, hair pigmentation, and problems relating to balance, vision, night blindness, thyroid, kidneys, heart, and infectious diseases like meningitis, antibiotic usage, injury, and typhoid. The pedigree structures were based upon interviews with multiple family members, and pedigrees of the enrolled families were drawn using Cyrillic program (version 2.1). All families showed recessive mode of inheritance. I studied 8 families of these 10. For linkage analyses, studies for DFNB1 locus, 3 STR markers (D13S175, D13S292, and D13S787) were genotyped using polyacrylamide gel electrophoresis (PAGE) and haplotypes were constructed to determined, linkage with DFNB1 locus. From a total of 8 families, a single family-10 showed linkage to DFNB1 locus.
PMCID: PMC3491296  PMID: 23162298
Deafness; gene GJB2; linkage analysis; locus DFNB1
21.  PedMerge: merging pedigrees to facilitate family-based genetic statistical analyses 
Bioinformatics  2010;26(21):2790-2791.
Summary: PedMerge allows users to accurately and efficiently merge separately ascertained pedigrees that belong to the same extended family. In addition to validation checks of pedigree structure, the software provides files in LINKAGE or PEDSYS format that easily allow to be used by a variety of genetic statistical software packages including LINKAGE, SOLAR, SLINK or can be further manipulated with Mega2.
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC2981498  PMID: 20843958
22.  When Family Means More (or Less) Than Genetics 
There is renewed interest in the use of family history to predict individual disease susceptibility, and as a result, standardized online family history tools are being developed and marketed as a “new genetic test.” It is not known how cultural variations in definitions of family influence collection of these data or what is the best format to use. This is significant given that the populations who carry the greatest burden of the target diseases have not been considered in efforts to test these tools. A qualitative study with a convenience sample of 19 Japanese Americans and Samoan Americans, two groups at high risk for type 2 diabetes, was conducted to explore the process of collecting family history. A particularly strong finding was the high degree of acceptance experienced by the participants with the process and their pride in visualizing their family graphically displayed in pedigrees. It was also found that Samoans included those linked by nonbiological ties in their families, which reflects their cultural practices. Further research is needed to assess the most effective and efficient way to gather family history given the complexities surrounding the deceptively simple concept of family.
PMCID: PMC2773542  PMID: 19398610
Pacific Islander; Samoan; Japanese American; family history; genetics; diabetes
23.  Compelling Evidence for a Prostate Cancer Gene at 22q12.3 by the International Consortium for Prostate Cancer Genetics 
Human molecular genetics  2007;16(11):1271-1278.
Previously, an analysis of 14 extended, high-risk Utah pedigrees localized the chromosome 22q linkage region to 3.2 Mb at 22q12.3-13.1 (flanked on each side by three recombinants), which contained 31 annotated genes. In this large, multi-centered, collaborative study, we performed statistical recombinant mapping in fifty-four pedigrees selected to be informative for recombinant mapping from nine member groups of the International Consortium for Prostate Cancer Genetics (ICPCG). These 54 pedigrees included the 14 extended pedigrees from Utah and 40 pedigrees from eight other ICPCG member groups. The additional 40 pedigrees were selected from a total pool of 1,213 such that each pedigree was required to both contain at least four prostate cancer (PRCA) cases and exhibit evidence for linkage to the chromosome 22q region. The recombinant events in these 40 independent pedigrees confirmed the previously proposed region. Further, when all 54 pedigrees were considered, the three-recombinant consensus region was narrowed by more than a megabase to 2.2 Mb at chromosome 22q12.3 flanked by D22S281 and D22S683. This narrower region eliminated 20 annotated genes from that previously proposed, leaving only eleven genes. This region at 22q12.3 is the most consistently identified and smallest linkage region for PRCA. This collaborative study by the ICPCG illustrates the value of consortium efforts and the continued utility of linkage analysis using informative pedigrees to localize genes for complex diseases.
PMCID: PMC2653215  PMID: 17478474
24.  Bimodal expressivity in dominant retinitis pigmentosa genetically linked to chromosome 19q. 
A clinical, psychophysical, and electrophysiologic study was undertaken of two autosomal dominant retinitis pigmentosa pedigrees with a genetic mutation assigned to chromosome 19q by linkage analysis. Members with the abnormal haplotype were either symptomatic with adolescent onset nyctalopia, restricted visual fields, and non-detectable electroretinographic responses by 30 years of age, or asymptomatic with normal fundus appearance and minimal or no psychophysical or electroretinographic abnormalities. There was no correlation in the severity in parents and their offspring. Pedigree analysis suggested that although the offspring of parents with the genetic mutation were at 50% risk of having the genetic defect, the risk of being symptomatic during a working lifetime was only 31%. Such bimodal phenotypic expressivity in these particular pedigrees may be explained by a second, allelic genetic influence and may be a phenomenon unique to this genetic locus. Genetic counselling in families expressing this phenotype can only be based on haplotype analysis since clinical investigations, even in the most elderly, would not preclude the presence of the mutant gene.
PMCID: PMC505271  PMID: 7488604
25.  Karyotyping, dermatoglyphic, and sweat pore analysis of five families affected with ectodermal dysplasia 
Hereditary ectodermal dysplasia is a genetic recessive trait characterized by hypohydrosis, hypotrichosis, and hypodontia. The affected individual show characteristic physiognomy like protruded forehead, depressed nasal bridge, periorbital wrinkling, protruded lips, etc. There is marked decrease in sweat and salivary secretion. Due to skin involvement palm and sole ridge patterns are disrupted.
In this study an attempt has been made to classify the affected members according to the degree of penetrance by pedigree analysis and also study karyotyping for cytogenetics, dermatoglyphic analysis for the various ridge patterns and variations in the number of sweat glands by sweat pore analysis in affected individuals.
Materials and Methods:
A total of five families who were affected with ectodermal dysplasia were considered. Pedigree analysis was drawn up to three generation by obtaining history. Dermatoglyphics and sweat pore analysis was done by obtaining palm and finger print impression using stamp pad ink. Karyotyping was done by collecting 3–5 ml peripheral blood. Karyotyping was prepared using lymphocyte culture. Chromosomes were examined at 20 spreads selected randomly under ×100 magnification. Results were analyzed by calculating mean values and percentage was obtained.
Karyotyping did not show any abnormalities, dermatoglyphic analysis and sweat pore counts showed marked variations when compared with normal. Moreover, pedigree analysis confirmed the status of the disease as that of the recessive trait.
Large number of affected patients needs to be evaluated for dermatoglypic analysis. Genetic aspect of the disease needs to be looked into the molecular level in an attempt to locate the gene locus responsible for ectodermal dysplasia and its manifestation.
PMCID: PMC3519214  PMID: 23248471
Dermatoglyphic; ectodermal dysplasia; karyotyping; pedigree analysis; sweat pore analysis

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