The role of large pedigrees in an era of high-throughput sequencing

[1]  Jennifer Williamson,et al.  Rare Variants in APP, PSEN1 and PSEN2 Increase Risk for AD in Late-Onset Alzheimer's Disease Families , 2012, PloS one.

[2]  E. Wijsman,et al.  Estimation and Visualization of Identity-by-Descent within Pedigrees Simplifies Interpretation of Complex Trait Analysis , 2011, Human Heredity.

[3]  Alexander F. Wilson,et al.  Linkage Analysis in the Next-Generation Sequencing Era , 2011, Human Heredity.

[4]  Alexander F. Wilson,et al.  Old lessons learned anew: family-based methods for detecting genes responsible for quantitative and qualitative traits in the Genetic Analysis Workshop 17 mini-exome sequence data , 2011, BMC proceedings.

[5]  M. Lemire,et al.  Successful identification of rare variants using oligogenic segregation analysis as a prioritizing tool for whole-exome sequencing studies , 2011, BMC proceedings.

[6]  I. Ionita-Laza,et al.  Study Designs for Identification of Rare Disease Variants in Complex Diseases: The Utility of Family-Based Designs , 2011, Genetics.

[7]  Dan Geiger,et al.  Integration of SNP genotyping confidence scores in IBD inference , 2011, Bioinform..

[8]  Melanie Bahlo,et al.  Reducing the exome search space for Mendelian diseases using genetic linkage analysis of exome genotypes , 2011, Genome Biology.

[9]  M. Rieder,et al.  Exome Sequencing Identifies SMAD3 Mutations as a Cause of Familial Thoracic Aortic Aneurysm and Dissection With Intracranial and Other Arterial Aneurysms , 2011, Circulation research.

[10]  M. Weedon,et al.  Exome sequencing identifies a DYNC1H1 mutation in a large pedigree with dominant axonal Charcot-Marie-Tooth disease. , 2011, American journal of human genetics.

[11]  J. Nadeau,et al.  Deep congenic analysis identifies many strong, context-dependent QTLs, one of which, Slc35b4, regulates obesity and glucose homeostasis. , 2011, Genome research.

[12]  E. Thompson The Structure of Genetic Linkage Data: From LIPED to 1M SNPs , 2011, Human Heredity.

[13]  Gonçalo R. Abecasis,et al.  Fine Mapping of Five Loci Associated with Low-Density Lipoprotein Cholesterol Detects Variants That Double the Explained Heritability , 2011, PLoS genetics.

[14]  W. Reardon,et al.  Gain-of-function mutations of ARHGAP31, a Cdc42/Rac1 GTPase regulator, cause syndromic cutis aplasia and limb anomalies. , 2011, American journal of human genetics.

[15]  K. Whelan,et al.  Family studies in Crohn's disease: new horizons in understanding disease pathogenesis, risk and prevention , 2011, Gut.

[16]  Yaniv Erlich,et al.  Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis. , 2011, Genome research.

[17]  Carol A. Bocchini,et al.  A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®) , 2011, Human mutation.

[18]  Deborah A Nickerson,et al.  Genome-wide studies of copy number variation and exome sequencing identify rare variants in BAG3 as a cause of dilated cardiomyopathy. , 2011, American journal of human genetics.

[19]  C I Amos,et al.  Evolutionary evidence of the effect of rare variants on disease etiology , 2011, Clinical genetics.

[20]  Xin Jin,et al.  TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing. , 2010, Brain : a journal of neurology.

[21]  Jonathan C. Cohen,et al.  Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia. , 2010, The New England journal of medicine.

[22]  Ana Morales,et al.  Clinical and genetic issues in dilated cardiomyopathy: A review for genetics professionals , 2010, Genetics in Medicine.

[23]  Nicholette D. Palmer,et al.  Molecular basis of a linkage peak: exome sequencing and family-based analysis identify a rare genetic variant in the ADIPOQ gene in the IRAS Family Study. , 2010, Human molecular genetics.

[24]  M. King,et al.  Genetic Heterogeneity in Human Disease , 2010, Cell.

[25]  E. Wijsman,et al.  Linkage and association analyses identify a candidate region for apoB level on chromosome 4q32.3 in FCHL families , 2010, Human Genetics.

[26]  L. Almasy,et al.  Sequence variation and genetic evolution at the human F12 locus: mapping quantitative trait nucleotides that influence FXII plasma levels. , 2010, Human molecular genetics.

[27]  P. Shannon,et al.  Exome sequencing identifies the cause of a Mendelian disorder , 2009, Nature Genetics.

[28]  Judy H. Cho,et al.  Finding the missing heritability of complex diseases , 2009, Nature.

[29]  F. Collins,et al.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits , 2009, Proceedings of the National Academy of Sciences.

[30]  T. Bird,et al.  Familial dyskinesia and facial myokymia (FDFM): Follow‐up of a large family and linkage to chromosome 3p21‐3q21 , 2009, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

[31]  Jonathan Flint,et al.  Genetic architecture of quantitative traits in mice, flies, and humans. , 2009, Genome research.

[32]  S E Humphries,et al.  Update and Analysis of the University College London Low Density Lipoprotein Receptor Familial Hypercholesterolemia Database , 2008, Annals of human genetics.

[33]  W. Bodmer,et al.  Common and rare variants in multifactorial susceptibility to common diseases , 2008, Nature Genetics.

[34]  Gregory Leibon,et al.  A SNP Streak Model for the Identification of Genetic Regions Identical-by-descent , 2008, Statistical applications in genetics and molecular biology.

[35]  Francis S Collins,et al.  A HapMap harvest of insights into the genetics of common disease. , 2008, The Journal of clinical investigation.

[36]  K Allen-Brady,et al.  Shared Genomic Segment Analysis. Mapping Disease Predisposition Genes in Extended Pedigrees Using SNP Genotype Assays , 2008, Annals of human genetics.

[37]  Francisco M De La Vega,et al.  A second-generation combined linkage physical map of the human genome. , 2007, Genome research.

[38]  E. Thompson,et al.  Multilocus Lod Scores in Large Pedigrees: Combination of Exact and Approximate Calculations , 2007, Human Heredity.

[39]  C. Jaquish,et al.  The Framingham Heart Study, on its way to becoming the gold standard for Cardiovascular Genetic Epidemiology? , 2007, BMC Medical Genetics.

[40]  Alun Thomas,et al.  Towards Linkage Analysis with Markers in Linkage Disequilibrium by Graphical Modelling , 2007, Human Heredity.

[41]  G. Schellenberg,et al.  Accounting for Linkage Disequilibrium among Markers in Linkage Analysis: Impact of Haplotype Frequency Estimation and Molecular Haplotypes for a Gene in a Candidate Region for Alzheimer’s Disease , 2007, Human Heredity.

[42]  Ellen M Wijsman,et al.  Multipoint linkage analysis with many multiallelic or dense diallelic markers: Markov chain-Monte Carlo provides practical approaches for genome scans on general pedigrees. , 2006, American journal of human genetics.

[43]  Joshua T. Burdick,et al.  In silico method for inferring genotypes in pedigrees , 2006, Nature Genetics.

[44]  Larry Wasserman,et al.  Using linkage genome scans to improve power of association in genome scans. , 2006, American journal of human genetics.

[45]  W. Kendall,et al.  Markov Chain Monte Carlo: Innovations And Applications , 2006 .

[46]  G. Abecasis,et al.  Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. , 2005, American journal of human genetics.

[47]  J. Ott,et al.  Complement Factor H Polymorphism in Age-Related Macular Degeneration , 2005, Science.

[48]  Nandita Mukhopadhyay,et al.  Comparative Study of Multipoint Methods for Genotype Error Detection , 2005, Human Heredity.

[49]  M. Sillanpää,et al.  Replication in genetic studies of complex traits , 2004, Annals of human genetics.

[50]  Jonathan C. Cohen,et al.  Multiple Rare Alleles Contribute to Low Plasma Levels of HDL Cholesterol , 2004, Science.

[51]  Leena Peltonen,et al.  Isolates and their potential use in complex gene mapping efforts. , 2004, Current opinion in genetics & development.

[52]  L. Almasy,et al.  Exploring Positional Candidate Genes: Linkage Conditional on Measured Genotype , 2004, Behavior genetics.

[53]  L. Peltonen,et al.  Combined analysis of genome scans of dutch and finnish families reveals a susceptibility locus for high-density lipoprotein cholesterol on chromosome 16q. , 2003, American journal of human genetics.

[54]  D. Botstein,et al.  Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease , 2003, Nature Genetics.

[55]  D E Weeks,et al.  Multipoint Estimation of Identity-by-Descent Probabilities at Arbitrary Positions among Marker Loci on General Pedigrees , 2001, Human Heredity.

[56]  Alun Thomas,et al.  Multilocus linkage analysis by blocked Gibbs sampling , 2000, Stat. Comput..

[57]  N. Risch Searching for genetic determinants in the new millennium , 2000, Nature.

[58]  Mario Pirastu,et al.  Population choice in mapping genes for complex diseases , 1999, Nature Genetics.

[59]  E. Wijsman,et al.  Multipoint oligogenic analysis of age-at-onset data with applications to Alzheimer disease pedigrees. , 1999, American journal of human genetics.

[60]  E. Wijsman,et al.  Linkage of low-density lipoprotein size to the lipoprotein lipase gene in heterozygous lipoprotein lipase deficiency. , 1999, American journal of human genetics.

[61]  Francis S. Collins,et al.  Variations on a Theme: Cataloging Human DNA Sequence Variation , 1997, Science.

[62]  S. Heath Markov chain Monte Carlo segregation and linkage analysis for oligogenic models. , 1997, American journal of human genetics.

[63]  M. Boehnke,et al.  Accurate inference of relationships in sib-pair linkage studies. , 1997, American journal of human genetics.

[64]  K Lange,et al.  Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker-sharing statistics. , 1996, American journal of human genetics.

[65]  G. Schellenberg,et al.  Candidate gene for the chromosome 1 familial Alzheimer's disease locus , 1995, Science.

[66]  D. Pollen,et al.  Cloning of a gene bearing missense mutations in early-onset familial Alzheimer's disease , 1995, Nature.

[67]  E. Wijsman,et al.  Genetic predictors of FCHL in four large pedigrees. Influence of ApoB level major locus predicted genotype and LDL subclass phenotype. , 1994, Arteriosclerosis and thrombosis : a journal of vascular biology.

[68]  Steven E. Bayer,et al.  A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. , 1994, Science.

[69]  M. Boehnke,et al.  Limits of resolution of genetic linkage studies: implications for the positional cloning of human disease genes. , 1994, American journal of human genetics.

[70]  E A Thompson,et al.  Monte Carlo likelihood in the genetic mapping of complex traits. , 1994, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[71]  E Sobel,et al.  Metropolis sampling in pedigree analysis , 1993, Statistical methods in medical research.

[72]  Manish S. Shah,et al.  A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes , 1993, Cell.

[73]  J. Ott,et al.  Strategies for characterizing highly polymorphic markers in human gene mapping. , 1992, American journal of human genetics.

[74]  Collins Fs,et al.  Of needles and haystacks: finding human disease genes by positional cloning. , 1991 .

[75]  K H Buetow,et al.  Influence of aberrant observations on high-resolution linkage analysis outcomes. , 1991, American journal of human genetics.

[76]  P. Savage,et al.  The Strong Heart Study. A study of cardiovascular disease in American Indians: design and methods. , 1990, American journal of epidemiology.

[77]  E. Wijsman A deductive method of haplotype analysis in pedigrees. , 1987, American journal of human genetics.

[78]  D. Botstein,et al.  Construction of a genetic linkage map in man using restriction fragment length polymorphisms. , 1980, American journal of human genetics.

[79]  J. Ott Estimation of the recombination fraction in human pedigrees: efficient computation of the likelihood for human linkage studies. , 1974, American journal of human genetics.

[80]  R. Elston,et al.  A general model for the genetic analysis of pedigree data. , 1971, Human heredity.

[81]  J. Thoday,et al.  Location of Polygenes , 1961, Nature.

[82]  N. Morton Sequential tests for the detection of linkage. , 1955, American journal of human genetics.

[83]  L. Penrose THE DETECTION OF AUTOSOMAL LINKAGE IN DATA WHICH CONSIST OF PAIRS OF BROTHERS AND SISTERS OF UNSPECIFIED PARENTAGE , 1935 .

[84]  A. Sturtevant,et al.  THE LINEAR ARRANGEMENT OF SIX SEX-LINKED FACTORS IN DROSOPHILA, AS SHOWN BY THEIR MODE OF ASSOCIATION , 1913 .

[85]  Thomas W. Mühleisen,et al.  The role of variation at AβPP, PSEN1, PSEN2, and MAPT in late onset Alzheimer's disease. , 2012, Journal of Alzheimer's disease : JAD.

[86]  Alexander F. Wilson,et al.  Lessons learned from Genetic Analysis Workshop 17: transitioning from genome‐wide association studies to whole‐genome statistical genetic analysis , 2011, Genetic epidemiology.

[87]  Tanya M. Teslovich,et al.  Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index , 2010 .

[88]  H. Koepke Efficient Testing Operations on Dynamic Graph Structures using Strong Hash Functions , 2010 .

[89]  G. Abecasis,et al.  Genotype imputation. , 2009, Annual review of genomics and human genetics.

[90]  Emily H Turner,et al.  Targeted Capture and Massively Parallel Sequencing of Twelve Human Exomes , 2009, Nature.

[91]  E. Wijsman,et al.  Summary of Genetic Analysis Workshop 15: Group 9 linkage analysis of the CEPH expression data , 2007, Genetic epidemiology.

[92]  E. Wijsman,et al.  Comparison of single‐nucleotide polymorphisms and microsatellite markers for linkage analysis in the COGA and simulated data sets for Genetic Analysis Workshop 14: Presentation Groups 1, 2, and 3 , 2005, Genetic epidemiology.

[93]  Elizabeth A. Thompson,et al.  MCMC IN THE ANALYSIS OF GENETIC DATA ON PEDIGREES , 2004 .

[94]  E. Wijsman,et al.  Genetic analysis of simulated oligogenic traits in nuclear and extended pedigrees: Summary of GAW10 contributions , 1997, Genetic epidemiology.

[95]  R W Cottingham,et al.  Error detection for genetic data, using likelihood methods. , 1996, American journal of human genetics.

[96]  F. Collins,et al.  Of needles and haystacks: finding human disease genes by positional cloning. , 1991, Clinical research.

[97]  L. Tsui,et al.  Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. , 1989, Science.

[98]  J. Haldane,et al.  A new estimate of the linkage between the genes for colourblindness and haemophilia in man. , 1947, Annals of eugenics.

[99]  P. Shannon,et al.  Supporting Online Material Materials and Methods Som Text Figs. S1 to S9 Tables S1 to S17 References Dataset S1 Analysis of Genetic Inheritance in a Family Quartet by Whole-genome Sequencing , 2022 .