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Open AccessGenomic analysis of 116 autism families strengthens known risk genes and highlights promising candidates
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic component in which rare variants contribute significantly to risk. We performed whole genome and/or exome sequenci...
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Article
Open AccessPangenome-based genome inference allows efficient and accurate genoty** across a wide spectrum of variant classes
Typical genoty** workflows map reads to a reference genome before identifying genetic variants. Generating such alignments introduces reference biases and comes with substantial computational burden. Further...
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Article
Recent ultra-rare inherited variants implicate new autism candidate risk genes
Autism is a highly heritable complex disorder in which de novo mutation (DNM) variation contributes significantly to risk. Using whole-genome sequencing data from 3,474 families, we investigate another source ...
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Article
Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing
Anthony Bleyer, Eric Lander, Mark Daly and colleagues show that frameshift mutations in a large VNTR of MUC1 cause medullary cystic kidney disease type 1. Their discovery sheds light on the biology of this diseas...
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Article
Structural haplotypes and recent evolution of the human 17q21.31 region
Steven McCarroll and colleagues use a population genetics approach to identify nine different structural forms of the 17q21.31 inversion region. They show that duplications have arisen independently on both an...
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Article
Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease
Mark Daly, Ramnik Xavier and colleagues report that a 20-kb deletion polymorphism upstream of IRGM is associated with altered IRGM expression and Crohn's disease. They also show that manipulation of IRGM levels i...
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Article
Evolutionary toggling of the MAPT 17q21.31 inversion region
Evan Eichler and colleagues present a sequence assembly of the inverted H2 haplotype of human chromosome 17q21.31 and show that the inversion is polymorphic in other great ape species. Their analyses suggest t...
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Article
Efficient map** of mendelian traits in dogs through genome-wide association
With several hundred genetic diseases and an advantageous genome structure, dogs are ideal for map** genes that cause disease. Here we report the development of a genoty** array with ∼27,000 SNPs and show ...
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Article
Common deletion polymorphisms in the human genome
The locations and properties of common deletion variants in the human genome are largely unknown. We describe a systematic method for using dense SNP genotype data to discover deletions and its application to ...