Detection of sharing by descent, long-range phasing and haplotype imputation.
paper
Cited
Public
- Authors
- Kong, Augustine; Masson, Gisli; Frigge, Michael L; Gylfason, Arnaldur; Zusmanovich, Pasha; Thorleifsson, Gudmar; Olason, Pall I; Ingason, Andres; Steinberg, Stacy; Rafnar, Thorunn; Sulem, Patrick; Mouy, Magali; Jonsson, Frosti; Thorsteinsdottir, Unnur; Gudbjartsson, Daniel F; Stefansson, Hreinn; Stefansson, Kari
- Year
- 2008
- Journal
- Nature genetics
- PMID
- 19165921
- DOI
- 10.1038/ng.216
- PMCID
- PMC4540081
Uncertainty about the phase of strings of SNPs creates complications in genetic analysis, although methods have been developed for phasing population-based samples. However, these methods can only phase a small number of SNPs effectively and become unreliable when applied to SNPs spanning many linkage disequilibrium (LD) blocks. Here we show how to phase more than 1,000 SNPs simultaneously for a large fraction of the 35,528 Icelanders genotyped by Illumina chips. Moreover, haplotypes that are identical by descent (IBD) between close and distant relatives, for example, those separated by ten meioses or more, can often be reliably detected. This method is particularly powerful in studies of the inheritance of recurrent mutations and fine-scale recombinations in large sample sets. A further extension of the method allows us to impute long haplotypes for individuals who are not genotyped.
The concept of surrogate parenthood. Typed relatives who share either the paternal or maternal haplotypes of the proband can be used to phase the proband as though they are actual parents. These relatives are referred to as surrogate fathers and surrogate mothers respectively. A surrogate father does not have to be a male and a surrogate mother does not have to be a female. Surrogate parenthood is locus specific. A sibling can be a surrogate father for one locus and a surrogate mother for another locus. However, for a locus where the sibling shares both haplotypes with the proband, the sibling is like a twin and cannot be used to phase the proband.
LLM interpretation
This is a conceptual diagram illustrating the principle of surrogate parenthood for genetic phasing. The figure shows a proband (bottom center) with blue and red haplotypes, linked to biological parents who are further connected via dashed lines to "surrogate fathers" (sharing the blue haplotype) and "surrogate mothers" (sharing the red haplotype). The visualization uses colored bars within circles and squares to represent specific haplotypes shared between the proband and various relatives.
As a function of sample size, in absolute number and as a fraction of the size of the living population in Iceland (316,000), (a) the fraction of typed individuals with at least one surrogate parent and (b) the fraction of individuals in the largest connected cluster in the haplotype sharing graph. A person with one or more surrogate parents can at least be partially phased. Individuals in the main cluster have a large number of surrogate relatives, and often every SNP can be phased.
LLM interpretation
This figure consists of two line graphs, (a) and (b), showing the fraction of individuals meeting specific phasing criteria as a function of the number of persons genotyped (0 to 35,000) and the corresponding percentage of the Icelandic population (0% to 10%). Both plots compare three genomic regions: MHC (10 Mb), 15q25 (10 Mb), and 15q25 (6.4 Mb). In both panels, the fraction increases sharply as sample size grows, asymptotically approaching 1.0, with the 15q25 (6.4 Mb) region generally showing the highest fraction.
Applying long-range phasing to determine a recombination event. The results from phasing a 10Mb region including the MHC were used, although only the 10 SNPs around the recombination event are highlighted. By phasing M using relatives R1 to R4, the recombination event in C3 could be deduced based on data from the trio F, M and C3 only, without the need of data from C1 and C2, or data from the parents of M. Having R2 and R4 could actually be better than having the two parents of M. A SNP informative for recombination in the children has to be heterozygous in M. Here both SNP5 and SNP6 are. To phase M, one of her parents (if typed) or surrogate relatives needs to be homozygous. In this case, R2 and R4 are each homozygous for both SNP5 and SNP6, so having one of them would be sufficient to deduce the precise location of the recombination. By contrast, R1 is homozygous at SNP6, but heterozygous at SNP5. With R1 only, we could deduce that a recombination in C3 occurred between SNP3 (the closest marker on the left that is heterozygous for M and homozygous for R1) and SNP6, but some resolution would be lost. The same could happen if one or both parents of M were typed. Surrogate relatives who are not surrogate parents of M can also help. E.g. the uncertain phase of SNP 5 in R1 can be resolved by surrogate parents of his sharing the other haplotype. Surrogate parents of R1 are surrogate relatives of M with ErdΓΆs distance 2.
LLM interpretation
This figure is a pedigree diagram combined with haplotype maps showing the use of long-range phasing to identify a recombination event. It displays the genotypes of 10 SNPs for a family (parents F and M, children C1, C2, C3) and several relatives (R1βR4), with alleles represented by colored vertical bars. The visualization highlights a recombination event in child C3, where the haplotype switches between the maternal alleles inherited from M.
The inheritance of a chromosome associated with a deletion. Typed are P1-P2 and R1-R3. Long-range phasing revealed that they all share a haplotype with over 1000 SNPs, although only P1 and P2 carry the deletion. Displayed are alleles of every 3rd of the first 100 SNPs on chromosome 15, including 17 of the 51 SNPs deleted. It can be inferred from the family structure that the shared region was transmitted to P1 and P2 through GGM and GF. Note: with only two typed SNPs (one shown) on the left of the deletion, the first two SNPs might only be IBS and not IBD between R1-R3 and P1-P2 as it could not be ruled out that a recombination event close by had taken place at one of the intermediary meioses, particularly since it is known that a recombination often accompanies a deletion event23.
LLM interpretation
This figure consists of a family pedigree diagram paired with a haplotype map showing SNP alleles for individuals R1, R2, R3, P1, and P2. The pedigree tracks the inheritance of a chromosomal region from a great-grandmother (GGM) and grandfather (GF), with arrows indicating where a *de novo* deletion likely occurred. The haplotype map displays a shared sequence of nucleotides (C, T, C, etc.) across all five individuals, with a gap labeled "deletion" specifically present in the bars for P1 and P2.
Imputing haplotypes into an untyped proband P. One of his children (C1) and 10 of his grandchildren (GC1 to GC10) are chip-typed (in blue). A region on 15q25 with 1001 typed SNPs centred at rs1051730 was investigated. All typed individuals were phased although only three haplotypes, HA , HB and HC, are highlighted. Haplotype HA could be imputed into P because C1 and GC10, descendants of P with different mates share HA IBD, satisfying Conditions 1 and 3. R2 shares HB IBD with GC3 and GC4, satisfying Conditions 1 and 2, and allow us to impute HB into P. However, as an exception to Conditions 2 and 3, HB can actually be imputed into P in an alternative way that does not require R2 and only employs the data from the descendants. Given that GC3 and GC4 share HB, it must be carried by either P or M1. The same with HC since it is shared by C1 and GC6. Given that GC4 and GC6 are related to P and M1 in the same way, HB and HC cannot both originate from M1. Since C1 has both HA and HC, and HA is established to be from P, HC must be from M1. This highlights that there could be extra information in addition to what can be deduced from the pair-wise sharing of relatives. Because R1 is related to P on his father side and R2 is a relative on his mother side, we can deduce that HA is the paternal haplotype of P and HB is the maternal haplotype, information useful for an imprinting model. While GC5, GC7, GC8 and GC9 do not play a role in the imputation of P here, they do contribute to the imputation of P for other regions in the genome. If C1 was not genotyped, GC1 and GC2 could be used to impute C1 and P.
LLM interpretation
This figure is a pedigree diagram illustrating the imputation of haplotypes for an untyped proband (P) using genetic data from relatives. The diagram shows the inheritance of three specific haplotypes ($H_A$, $H_B$, and $H_C$) across three generations, with chip-typed individuals highlighted in blue. Vertical sequences of nucleotides (A, G, C, T) are displayed for several descendants (GC1βGC10) and the child (C1), with color-coded highlights indicating shared haplotype segments.
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| Identification of sequence variants influencing immunoglobulin levels. | Jonsson S et al. | β | 2017 | β |
| Phased Genome Sequencing Through Chromosome Sorting. | Chen X et al. | β | 2017 | β |
| Reproductive fitness and genetic risk of psychiatric disorders in the general population. | Mullins N et al. | β | 2017 | β |
| Revealing allele-specific gene expression by single-cell transcriptomics. | Benitez JA et al. | β | 2017 | β |
| Sequence variant at 4q25 near PITX2 associates with appendicitis. | Kristjansson RP et al. | β | 2017 | β |
| Sequence variants in ARHGAP15, COLQ and FAM155A associate with diverticular disease and diverticulitis. | Sigurdsson S et al. | β | 2017 | β |
| Use of haplotypes to identify regions harbouring lethal recessive variants in pigs. | Howard DM et al. | β | 2017 | β |
| Whole-genome sequencing identifies rare genotypes in COMP and CHADL associated with high risk of hip osteoarthritis. | Styrkarsdottir U et al. | β | 2017 | β |
| A practical approach to detect ancestral haplotypes in livestock populations. | SΓ‘nchez-Molano E et al. | β | 2016 | β |
| A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis. | Rivas MA et al. | β | 2016 | β |
| Assigning breed origin to alleles in crossbred animals. | Vandenplas J et al. | β | 2016 | β |
| Atlas of Cryptic Genetic Relatedness Among 1000 Human Genomes. | Fedorova L et al. | β | 2016 | β |
| Common and rare variants associating with serum levels of creatine kinase and lactate dehydrogenase. | Kristjansson RP et al. | β | 2016 | β |
| Common variants upstream of KDR encoding VEGFR2 and in TTC39B associate with endometriosis. | Steinthorsdottir V et al. | β | 2016 | β |
| Conflation of Short Identity-by-Descent Segments Bias Their Inferred Length Distribution. | Chiang CW et al. | β | 2016 | β |
| Epigenetic and genetic components of height regulation. | Benonisdottir S et al. | β | 2016 | β |
| Fast and accurate long-range phasing in a UK Biobank cohort. | Loh PR et al. | β | 2016 | β |
| Haplotype estimation for biobank-scale data sets. | O'Connell J et al. | β | 2016 | β |
| Imputation Accuracy from Low to Moderate Density Single Nucleotide Polymorphism Chips in a Thai Multibreed Dairy Cattle Population. | Jattawa D et al. | β | 2016 | β |
| InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms. | Patel A et al. | β | 2016 | β |
| Insertion of an SVA-E retrotransposon into the CASP8 gene is associated with protection against prostate cancer. | Stacey SN et al. | β | 2016 | β |
| Multi-nucleotide de novo Mutations in Humans. | Besenbacher S et al. | β | 2016 | β |
| New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era. | Gao F et al. | β | 2016 | β |
| Phasing for medical sequencing using rare variants and large haplotype reference panels. | Sharp K et al. | β | 2016 | β |
| Reference-based phasing using the Haplotype Reference Consortium panel. | Loh PR et al. | β | 2016 | β |
| Sequence variants in the PTCH1 gene associate with spine bone mineral density and osteoporotic fractures. | Styrkarsdottir U et al. | β | 2016 | β |
| The Tohoku Medical Megabank Project: Design and Mission. | Kuriyama S et al. | β | 2016 | β |
| Two Rare Mutations in the COL1A2 Gene Associate With Low Bone Mineral Density and Fractures in Iceland. | Styrkarsdottir U et al. | β | 2016 | β |
| Variants with large effects on blood lipids and the role of cholesterol and triglycerides in coronary disease. | Helgadottir A et al. | β | 2016 | β |
| A Splice Region Variant in LDLR Lowers Non-high Density Lipoprotein Cholesterol and Protects against Coronary Artery Disease. | Gretarsdottir S et al. | β | 2015 | β |
| Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae. | Redmond SN et al. | β | 2015 | β |
| Common and rare variants associated with kidney stones and biochemical traits. | Oddsson A et al. | β | 2015 | β |
| EIF4G1 is neither a strong nor a common risk factor for Parkinson's disease: evidence from large European cohorts. | Huttenlocher J et al. | β | 2015 | β |
| Family genome browser: visualizing genomes with pedigree information. | Juan L et al. | β | 2015 | β |
| GENLIB: an R package for the analysis of genealogical data. | Gauvin H et al. | β | 2015 | β |
| GenomeLaser: fast and accurate haplotyping from pedigree genotypes. | Li W et al. | β | 2015 | β |
| Genome-wide meta-analysis reveals common splice site acceptor variant in CHRNA4 associated with nicotine dependence. | Hancock DB et al. | β | 2015 | β |
| HaploShare: identification of extended haplotypes shared by cases and evaluation against controls. | Ying D et al. | β | 2015 | β |
| Heterozygote carriers for CNVs in PARK2 are at increased risk of Parkinson's disease. | Huttenlocher J et al. | β | 2015 | β |
| Indications for potential parent-of-origin effects within the FTO gene. | Liu X et al. | β | 2015 | β |
| Large-scale whole-genome sequencing of the Icelandic population. | Gudbjartsson DF et al. | β | 2015 | β |
| Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates. | Palamara PF et al. | β | 2015 | β |
| Loss-of-function variants in ABCA7 confer risk of Alzheimer's disease. | Steinberg S et al. | β | 2015 | β |
| Loss-of-function variants in ATM confer risk of gastric cancer. | Helgason H et al. | β | 2015 | β |
| New basal cell carcinoma susceptibility loci. | Stacey SN et al. | β | 2015 | β |
| Parente2: a fast and accurate method for detecting identity by descent. | Rodriguez JM et al. | β | 2015 | β |
| Pedigree-Free Descent-Based Gene Mapping from Population Samples. | Glazner C et al. | β | 2015 | β |
| PRIMAL: Fast and accurate pedigree-based imputation from sequence data in a founder population. | Livne OE et al. | β | 2015 | β |
| Privacy in the Genomic Era. | Naveed M et al. | β | 2015 | β |
| Progress and promise in understanding the genetic basis of common diseases. | Price AL et al. | β | 2015 | β |
| Relatedness in the post-genomic era: is it still useful? | Speed D et al. | β | 2015 | β |
| Sequence variants from whole genome sequencing a large group of Icelanders. | Gudbjartsson DF et al. | β | 2015 | β |
| Small island, big genetic discoveries. | Lettre G et al. | β | 2015 | β |
| The genome as pharmacopeia: association of genetic dose with phenotypic response. | Wadhawan S et al. | β | 2015 | β |
| Variants in ELL2 influencing immunoglobulin levels associate with multiple myeloma. | Swaminathan B et al. | β | 2015 | β |
| Whole genome SNP genotype piecemeal imputation. | Wang Y et al. | β | 2015 | β |
| A general approach for haplotype phasing across the full spectrum of relatedness. | O'Connell J et al. | β | 2014 | β |
| A new approach for efficient genotype imputation using information from relatives. | Sargolzaei M et al. | β | 2014 | β |
| A renewal theory approach to IBD sharing. | Carmi S et al. | β | 2014 | β |
| Common and low-frequency variants associated with genome-wide recombination rate. | Kong A et al. | β | 2014 | β |
| Detection of recombination events, haplotype reconstruction and imputation of sires using half-sib SNP genotypes. | Ferdosi MH et al. | β | 2014 | β |
| Gene-Lifestyle Interactions in Complex Diseases: Design and Description of the GLACIER and VIKING Studies. | Kurbasic A et al. | β | 2014 | β |
| Genetic characterization of Greek population isolates reveals strong genetic drift at missense and trait-associated variants. | Panoutsopoulou K et al. | β | 2014 | β |
| Genome-wide association study yields variants at 20p12.2 that associate with urinary bladder cancer. | Rafnar T et al. | β | 2014 | β |
| Genome-wide patterns of identity-by-descent sharing in the French Canadian founder population. | Gauvin H et al. | β | 2014 | β |
| Germline sequence variants in TGM3 and RGS22 confer risk of basal cell carcinoma. | Stacey SN et al. | β | 2014 | β |
| Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. | Amini S et al. | β | 2014 | β |
| Identification of key ancestors of modern germplasm in a breeding program of maize. | Technow F et al. | β | 2014 | β |
| Identification of low-frequency and rare sequence variants associated with elevated or reduced risk of type 2 diabetes. | Steinthorsdottir V et al. | β | 2014 | β |
| Joint inference of identity by descent along multiple chromosomes from population samples. | Zheng C et al. | β | 2014 | β |
| KmerStream: streaming algorithms for k-mer abundance estimation. | Melsted P et al. | β | 2014 | β |
| Nationwide study on hypertrophic cardiomyopathy in Iceland: evidence of a MYBPC3 founder mutation. | Adalsteinsdottir B et al. | β | 2014 | β |
| PedBLIMP: extending linear predictors to impute genotypes in pedigrees. | Chen W et al. | β | 2014 | β |
| Power of family-based association designs to detect rare variants in large pedigrees using imputed genotypes. | Saad M et al. | β | 2014 | β |
| Rare missense variants in POT1 predispose to familial cutaneous malignant melanoma. | Shi J et al. | β | 2014 | β |
| Rare mutations associating with serum creatinine and chronic kidney disease. | Sveinbjornsson G et al. | β | 2014 | β |
| Recombination locations and rates in beef cattle assessed from parent-offspring pairs. | Weng ZQ et al. | β | 2014 | β |
| Reducing pervasive false-positive identical-by-descent segments detected by large-scale pedigree analysis. | Durand EY et al. | β | 2014 | β |
| Routes for breaching and protecting genetic privacy. | Erlich Y et al. | β | 2014 | β |
| Severe osteoarthritis of the hand associates with common variants within the ALDH1A2 gene and with rare variants at 1p31. | Styrkarsdottir U et al. | β | 2014 | β |
| Using population isolates in genetic association studies. | Hatzikotoulas K et al. | β | 2014 | β |
| Whole-genome haplotyping approaches and genomic medicine. | Glusman G et al. | β | 2014 | β |
| Accuracy of genomic prediction using an evenly spaced, low-density single nucleotide polymorphism panel in broiler chickens. | Wang C et al. | β | 2013 | β |
| ACCURATE CONSTRUCTION OF LONG RANGE HAPLOTYPE IN UNRELATED INDIVIDUALS. | Johnson NA et al. | β | 2013 | β |
| A common variant at 8q24.21 is associated with renal cell cancer. | Gudmundsson J et al. | β | 2013 | β |
| A polymorphism in IRF4 affects human pigmentation through a tyrosinase-dependent MITF/TFAP2A pathway. | Praetorius C et al. | β | 2013 | β |
| A rare functional cardioprotective APOC3 variant has risen in frequency in distinct population isolates. | Tachmazidou I et al. | β | 2013 | β |
| A rare nonsynonymous sequence variant in C3 is associated with high risk of age-related macular degeneration. | Helgason H et al. | β | 2013 | β |
| Assets of imputation to ultra-high density for productive and functional traits. | JimΓ©nez-Montero JA et al. | β | 2013 | β |
| Extending long-range phasing and haplotype library imputation methods to impute genotypes on sex chromosomes. | Hickey JM et al. | β | 2013 | β |
| From genetic discovery to future personalized health research. | Palotie A et al. | β | 2013 | β |
| Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets. | Grarup N et al. | β | 2013 | β |
| Genomic evaluations using similarity between haplotypes. | Hickey JM et al. | β | 2013 | β |
| Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold. | Menelaou A et al. | β | 2013 | β |
| Genotype imputation via matrix completion. | Chi EC et al. | β | 2013 | β |
| Genotype phasing in populations of closely related individuals. | Hickey JM | β | 2013 | β |
| GIGI: an approach to effective imputation of dense genotypes on large pedigrees. | Cheung CY et al. | β | 2013 | β |
| Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations. | Gomez-Raya L et al. | β | 2013 | β |
| Hunting human disease genes: lessons from the past, challenges for the future. | Brunham LR et al. | β | 2013 | β |
| Identity-by-descent-based heritability analysis in the Northern Finland Birth Cohort. | Browning SR et al. | β | 2013 | β |
| Identity by descent: variation in meiosis, across genomes, and in populations. | Thompson EA | β | 2013 | β |
| Improving the accuracy and efficiency of identity-by-descent detection in population data. | Browning BL et al. | β | 2013 | β |
| Inference of identity by descent in population isolates and optimal sequencing studies. | Glodzik D et al. | β | 2013 | β |
| Intellectual disability is associated with increased runs of homozygosity in simplex autism. | Gamsiz ED et al. | β | 2013 | β |
| Small effective population size and genetic homogeneity in the Val Borbera isolate. | Colonna V et al. | β | 2013 | β |
| SNP linkage analysis and whole exome sequencing identify a novel POU4F3 mutation in autosomal dominant late-onset nonsyndromic hearing loss (DFNA15). | Kim HJ et al. | β | 2013 | β |
| The variance of identity-by-descent sharing in the Wright-Fisher model. | Carmi S et al. | β | 2013 | β |
| Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits. | Zaitlen N et al. | β | 2013 | β |
| Utilizing graph theory to select the largest set of unrelated individuals for genetic analysis. | Staples J et al. | β | 2013 | β |
| Accuracy of genotype imputation in sheep breeds. | Hayes BJ et al. | β | 2012 | β |
| Accurate imputation of rare and common variants in a founder population from a small number of sequenced individuals. | Uricchio LH et al. | β | 2012 | β |
| Alzheimer's disease: A protective mutation. | De Strooper B et al. | β | 2012 | β |
| A mutation in APP protects against Alzheimer's disease and age-related cognitive decline. | Jonsson T et al. | β | 2012 | β |
| An ensemble-based approach to imputation of moderate-density genotypes for genomic selection with application to Angus cattle. | Sun C et al. | β | 2012 | β |
| A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation. | Hickey JM et al. | β | 2012 | β |
| Apolipoprotein(a) genetic sequence variants associated with systemic atherosclerosis and coronary atherosclerotic burden but not with venous thromboembolism. | Helgadottir A et al. | β | 2012 | β |
| A study based on whole-genome sequencing yields a rare variant at 8q24 associated with prostate cancer. | Gudmundsson J et al. | β | 2012 | β |
| Cryptic distant relatives are common in both isolated and cosmopolitan genetic samples. | Henn BM et al. | β | 2012 | β |
| Detecting identity by descent and homozygosity mapping in whole-exome sequencing data. | Zhuang Z et al. | β | 2012 | β |
| Detecting rare variant associations by identity-by-descent mapping in case-control studies. | Browning SR et al. | β | 2012 | β |
| Detection of identity by descent using next-generation whole genome sequencing data. | Su SY et al. | β | 2012 | β |
| Discovery of common variants associated with low TSH levels and thyroid cancer risk. | Gudmundsson J et al. | β | 2012 | β |
| Estimating recombination rates from genetic variation in humans. | Auton A et al. | β | 2012 | β |
| Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. | Howie B et al. | β | 2012 | β |
| Genetic predisposition of the severity of joint destruction in rheumatoid arthritis: a population-based study. | Knevel R et al. | β | 2012 | β |
| Identifying mutation regions for closely related individuals without a known pedigree. | Cui W et al. | β | 2012 | β |
| Identity by descent between distant relatives: detection and applications. | Browning SR et al. | β | 2012 | β |
| Imputation of rare variants in next-generation association studies. | Asimit JL et al. | β | 2012 | β |
| Phasing of many thousands of genotyped samples. | Williams AL et al. | β | 2012 | β |
| The architecture of long-range haplotypes shared within and across populations. | Gusev A et al. | β | 2012 | β |
| Variants in DENND1A are associated with polycystic ovary syndrome in women of European ancestry. | Welt CK et al. | β | 2012 | β |
| Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle. | Larkin DM et al. | β | 2012 | β |
| A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes. | Hickey JM et al. | β | 2011 | β |
| A common spinal muscular atrophy deletion mutation is present on a single founder haplotype in the US Hutterites. | Chong JX et al. | β | 2011 | β |
| A fast, powerful method for detecting identity by descent. | Browning BL et al. | β | 2011 | β |
| A germline variant in the TP53 polyadenylation signal confers cancer susceptibility. | Stacey SN et al. | β | 2011 | β |
| A rare variant in MYH6 is associated with high risk of sick sinus syndrome. | Holm H et al. | β | 2011 | β |
| Completely phased genome sequencing through chromosome sorting. | Yang H et al. | β | 2011 | β |
| Evolution and population genetics of exotic and re-emerging pathogens: novel tools and approaches. | GrΓΌnwald NJ et al. | β | 2011 | β |
| Genotype imputation with thousands of genomes. | Howie B et al. | β | 2011 | β |
| Haplotype phasing: existing methods and new developments. | Browning SR et al. | β | 2011 | β |
| Haplotype sharing test maps genes for familial cardiomyopathies. | van der Zwaag PA et al. | β | 2011 | β |
| Homozygosity mapping on a single patient: identification of homozygous regions of recent common ancestry by using population data. | Zhang L et al. | β | 2011 | β |
| Identification of low-frequency variants associated with gout and serum uric acid levels. | Sulem P et al. | β | 2011 | β |
| Identity-by-descent-based phasing and imputation in founder populations using graphical models. | Palin K et al. | β | 2011 | β |
| Identity by descent estimation with dense genome-wide genotype data. | Han L et al. | β | 2011 | β |
| Improved risk prediction for Crohn's disease with a multi-locus approach. | Kang J et al. | β | 2011 | β |
| Imputation of missing genotypes from sparse to high density using long-range phasing. | Daetwyler HD et al. | β | 2011 | β |
| Imputation of missing single nucleotide polymorphism genotypes using a multivariate mixed model framework. | Calus MP et al. | β | 2011 | β |
| Mapping rare and common causal alleles for complex human diseases. | Raychaudhuri S | β | 2011 | β |
| Modeling of identity-by-descent processes along a chromosome between haplotypes and their genotyped ancestors. | Druet T et al. | β | 2011 | β |
| Mutations in BRIP1 confer high risk of ovarian cancer. | Rafnar T et al. | β | 2011 | β |
| Next-generation association studies for complex traits. | Zeggini E | β | 2011 | β |
| Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals. | Price AL et al. | β | 2011 | β |
| The Clark phaseable sample size problem: long-range phasing and loss of heterozygosity in GWAS. | HalldΓ³rsson BV et al. | β | 2011 | β |
| The importance of phase information for human genomics. | Tewhey R et al. | β | 2011 | β |
| Accuracy of direct genomic values derived from imputed single nucleotide polymorphism genotypes in Jersey cattle. | Weigel KA et al. | β | 2010 | β |
| A hidden markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping. | Druet T et al. | β | 2010 | β |
| A sequence variant at 4p16.3 confers susceptibility to urinary bladder cancer. | Kiemeney LA et al. | β | 2010 | β |
| A two-stage approximation for analysis of mixture genetic models in large pedigrees. | Habier D et al. | β | 2010 | β |
| Common variants near CAV1 and CAV2 are associated with primary open-angle glaucoma. | Thorleifsson G et al. | β | 2010 | β |
| Fine-scale recombination rate differences between sexes, populations and individuals. | Kong A et al. | β | 2010 | β |
| General lessons from large-scale studies to identify human cancer predisposition genes. | Cazier JB et al. | β | 2010 | β |
| Genotype imputation for genome-wide association studies. | Marchini J et al. | β | 2010 | β |
| High-resolution detection of identity by descent in unrelated individuals. | Browning SR et al. | β | 2010 | β |
| Improved IBD detection using incomplete haplotype information. | Genovese G et al. | β | 2010 | β |
| Making a haplotype catalog with estimated frequencies based on SNP homozygotes. | Yamaguchi-Kabata Y et al. | β | 2010 | β |
| Missing heritability and strategies for finding the underlying causes of complex disease. | Eichler EE et al. | β | 2010 | β |
| Population structure and genome-wide patterns of variation in Ireland and Britain. | O'Dushlaine CT et al. | β | 2010 | β |
| Prediction of unobserved single nucleotide polymorphism genotypes of Jersey cattle using reference panels and population-based imputation algorithms. | Weigel KA et al. | β | 2010 | β |
| Reconciling the analysis of IBD and IBS in complex trait studies. | Powell JE et al. | β | 2010 | β |
| The use of family relationships and linkage disequilibrium to impute phase and missing genotypes in up to whole-genome sequence density genotypic data. | Meuwissen T et al. | β | 2010 | β |
| Whole genome sequencing. | Ng PC et al. | β | 2010 | β |
| A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. | Howie BN et al. | β | 2009 | β |
| Common variants conferring risk of schizophrenia. | Stefansson H et al. | β | 2009 | β |
| Disruption of the neurexin 1 gene is associated with schizophrenia. | Rujescu D et al. | β | 2009 | β |
| Finding the missing heritability of complex diseases. | Manolio TA et al. | β | 2009 | β |
| New common variants affecting susceptibility to basal cell carcinoma. | Stacey SN et al. | β | 2009 | β |
| Parental origin of sequence variants associated with complex diseases. | Kong A et al. | β | 2009 | β |
| Robust physical methods that enrich genomic regions identical by descent for linkage studies: confirmation of a locus for osteogenesis imperfecta. | Brooks P et al. | β | 2009 | β |
| Systematic haplotype analysis resolves a complex plasma plant sterol locus on the Micronesian Island of Kosrae. | Kenny EE et al. | β | 2009 | β |
| Whole population, genome-wide mapping of hidden relatedness. | Gusev A et al. | β | 2009 | β |
| Genome-wide association studies: potential next steps on a genetic journey. | McCarthy MI et al. | β | 2008 | β |