- Mapping the human reference genome's missing sequence by three-way admixture in Latino genomes
Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Am J Hum Genet 93:411-21. 2013
..Genome assembly efforts and future builds of the human genome reference will be strongly informed by this localization of genes and other euchromatic sequences that are embedded within highly repetitive pericentromeric regions. ..
- Improved IBD detection using incomplete haplotype information
Department of Mathematics, Dartmouth College, Hanover NH 03755, USA
BMC Genet 11:58. 2010
..The use of these platforms has enabled population-based genome-wide association studies. However, in inheritance-based studies, current methods do not take full advantage of the information present in such genotyping analyses...
- Using population admixture to help complete maps of the human genome
Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Nat Genet 45:406-14, 414e1-2. 2013
..We describe how knowledge of the locations of these sequences can inform disease association and genome biology studies...
- APOL1 variants and kidney disease in people of recent African ancestry
Stanley Center, Broad Institute, Cambridge, MA 02142, USA
Nat Rev Nephrol 9:240-4. 2013
..Although no biological evidence currently exists for the causality of APOL1 variants with kidney disease, our statistical reasoning provides a strong case for causality, and a region to target in future functional studies...
- Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates
Pier Francesco Palamara
Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA 02115, USA Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA Electronic address
Am J Hum Genet 97:775-89. 2015
..Our analysis suggests that a mutation-rate estimate higher than that reported by recent pedigree-based studies should be adopted in the context of DNA-based demographic reconstruction...
- Large multiallelic copy number variations in humans
Robert E Handsaker
1 Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 2 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 3 Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
Nat Genet 47:296-303. 2015
..We also describe partially successful initial strategies for analyzing mCNVs via imputation and provide an initial data resource to support such analyses. ..
- Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores
Bjarni J Vilhjálmsson
Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA 02115, USA Program in Genetic Epidemiology and Statistical Genetics, Harvard T H Chan School of Public Health, Boston, MA 02115, USA Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark Electronic address
Am J Hum Genet 97:576-92. 2015
..A similar relative improvement in accuracy was observed for three additional large disease datasets and for non-European schizophrenia samples. The advantage of LDpred over existing methods will grow as sample sizes increase. ..
- No evidence for rare recessive and compound heterozygous disruptive variants in schizophrenia
Douglas M Ruderfer
1 Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA 2 Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA 3 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Eur J Hum Genet 23:555-7. 2015
..We do not find evidence for association with SCZ, either genome wide or at specific loci. However, we note the possible impact of sample size and population genetic factors on the power to detect and quantify any burden that may exist. ..
- Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection
Harvard Massachusetts Institute of Technology MIT Division of Health, Science and Technology, Cambridge, USA
Am J Hum Genet 89:368-81. 2011
..The most significantly differentiated marker in our analysis, rs2920283, is highly differentiated in both Africa and East Asia and has prior genome-wide significant associations to bladder and gastric cancers...
- Frequency of rare allelic variation in candidate genes among individuals with low and high urinary calcium excretion
Hakan R Toka
Division of Nephrology, Brigham and Women s Hospital, Boston, Massachusetts, United States of America Division of Nephrology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
PLoS ONE 8:e71885. 2013
..In the tested set of candidate genes, rare allelic variants do not appear to contribute significantly to differences in urinary calcium excretion between individuals...