ArticlePLoS genetics2011
Phased whole-genome genetic risk in a family quartet using a major allele reference sequence.
Article in PLoS genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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Who cites it
86 citing papers in PubMed, 148 citations in OpenAlex.
- Outcomes of a Randomized Controlled Trial of Genomic Counseling for Patients Receiving Personalized and Actionable Complex Disease Reports.Journal of genetic counseling · 2017Trial
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- The complete and fully-phased diploid genome of a male Han Chinese.Cell research · 2023Article
- Variant calling and benchmarking in an era of complete human genome sequences.Nature reviews. Genetics · 2023Review
- Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses.Genome research · 2022Article
- A guide for the diagnosis of rare and undiagnosed disease: beyond the exome.Genome medicine · 2022Review
- Whole Exome Sequencing in South Africa: Stakeholder Views on Return of Individual Research Results and Incidental Findings.Frontiers in genetics · 2022Article
- An Evidence-Based Framework for Evaluating Pharmacogenomics Knowledge for Personalized Medicine.Clinical pharmacology and therapeutics · 2021Article
- Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference.Nature communications · 2021Article
- Reference flow: reducing reference bias using multiple population genomes.Genome biology · 2021Article
- Data Integration Challenges for Machine Learning in Precision Medicine.Frontiers in medicine · 2021Review
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- Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery.Genome biology · 2020Article
- The clinical and genetic characteristics of permanent neonatal diabetes (PNDM) in the state of Qatar.Molecular genetics & genomic medicine · 2019Article
- Is it time to change the reference genome?Genome biology · 2019Article
- hg19KIndel: ethnicity normalized human reference genome.BMC genomics · 2019Article
- Identification of an iron-responsive subtype in two children diagnosed with relapsing-remitting multiple sclerosis using whole exome sequencing.Molecular genetics and metabolism reports · 2019Article
- Review
- FORGe: prioritizing variants for graph genomes.Genome biology · 2018Article
- De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations.Nature communications · 2018Article
26 more citing papers are in PubMed but not listed here.
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Authors and funding
33 authors at 5 institutions in 1 country.
Funding
Abstract
Whole-genome sequencing harbors unprecedented potential for characterization of individual and family genetic variation. Here, we develop a novel synthetic human reference sequence that is ethnically concordant and use it for the analysis of genomes from a nuclear family with history of familial thrombophilia. We demonstrate that the use of the major allele reference sequence results in improved genotype accuracy for disease-associated variant loci. We infer recombination sites to the lowest median resolution demonstrated to date (< 1,000 base pairs). We use family inheritance state analysis to control sequencing error and inform family-wide haplotype phasing, allowing quantification of genome-wide compound heterozygosity. We develop a sequence-based methodology for Human Leukocyte Antigen typing that contributes to disease risk prediction. Finally, we advance methods for analysis of disease and pharmacogenomic risk across the coding and non-coding genome that incorporate phased variant data. We show these methods are capable of identifying multigenic risk for inherited thrombophilia and informing the appropriate pharmacological therapy. These ethnicity-specific, family-based approaches to interpretation of genetic variation are emblematic of the next generation of genetic risk assessment using whole-genome sequencing.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.