- The functional spectrum of low-frequency coding variation
Gabor T Marth
Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
Genome Biol 12:R84. 2011
- Next-generation sequencing for HLA typing of class I loci
Rachel L Erlich
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
BMC Genomics 12:42. 2011
..We have coupled this process to a novel HLA calling algorithm to determine the most likely pair of alleles at each locus...
- A framework for variation discovery and genotyping using next-generation DNA sequencing data
Mark A DePristo
Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
Nat Genet 43:491-8. 2011
..We here discuss the application of these tools, instantiated in the Genome Analysis Toolkit, to deep whole-genome, whole-exome capture and multi-sample low-pass (∼4×) 1000 Genomes Project datasets...
- Efficiency and power as a function of sequence coverage, SNP array density, and imputation
Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
PLoS Comput Biol 8:e1002604. 2012
..Our joint framework informs the use of next-generation sequencing in genome wide association studies and supports development of improved methods for genotype calling...
- Pacific biosciences sequencing technology for genotyping and variation discovery in human data
Mauricio O Carneiro
Broad Institute of MIT and Harvard, Medical and Population Genetics Program, Cambridge, MA 02141, USA
BMC Genomics 13:375. 2012
..With these potential advantages in mind, we here evaluate the utility of the Pacific Biosciences RS platform for human medical amplicon resequencing projects...
- The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
Genome Res 20:1297-303. 2010
- Mapping copy number variation by population-scale genome sequencing
Ryan E Mills
Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
Nature 470:59-65. 2011
..Our analytical framework and SV map serves as a resource for sequencing-based association studies...