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Method: Sequencing of isolated sperm cells for direct haplotyping of a human genome
- Ewen F. Kirkness,
- Rashel V. Grindberg,
- Joyclyn Yee-Greenbaum,
- Christian R. Marshall,
- Stephen W. Scherer,
- Roger S. Lasken,
- and J. Craig Venter
Genome Res. May 2013 23: 826-832; Published in Advance January 2, 2013, doi:10.1101/gr.144600.112
...HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, et al. 2009. Sequence and structural variation in a human uncovered by short-read, massively parallel ligation sequencing using two-base encoding.Genome Res 19: 1527–1541. McLaughlin HM, Sakaguchi R, Liu C...
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Method: Paired-end sequencing of Fosmid libraries by Illumina
- Louise J.S. Williams,
- Diana G. Tabbaa,
- Na Li,
- Aaron M. Berlin,
- Terrance P. Shea,
- Iain MacCallum,
- Michael S. Lawrence,
- Yotam Drier,
- Gad Getz,
- Sarah K. Young,
- David B. Jaffe,
- Chad Nusbaum,
- and Andreas Gnirke
Genome Res. November 2012 22: 2241-2249; Published in Advance July 16, 2012, doi:10.1101/gr.138925.112
.... Their consistent, narrow insert-size distribution centered around 35–40 kb enabled the scanning of individual human swith readpairs to detect structural variation such as insertions, deletions, and inversions (International Human Genome Sequencing Consortium 2004; Tuzun et al. 2005; Kidd et al. 2008). Massively...
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Resource: The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
- Aaron McKenna,
- Matthew Hanna,
- Eric Banks,
- Andrey Sivachenko,
- Kristian Cibulskis,
- Andrew Kernytsky,
- Kiran Garimella,
- David Altshuler,
- Stacey Gabriel,
- Mark Daly,
- and Mark A. DePristo
Genome Res. September 2010 20: 1297-1303; Published in Advance July 19, 2010, doi:10.1101/gr.107524.110
..., Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, et al. 2009. Sequence and structural variation in a human uncovered by short-read, massively parallel ligation sequencing using two-base encoding.Genome Res 19: 1527–1541. MorganM, Anders S, Lawrence M, Aboyoun...
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Method: Accurate and comprehensive sequencing of personal genomes
- Subramanian S. Ajay,
- Stephen C.J. Parker,
- Hatice Ozel Abaan,
- Karin V. Fuentes Fajardo,
- and Elliott H. Margulies
Genome Res. September 2011 21: 1498-1505; Published in Advance July 19, 2011, doi:10.1101/gr.123638.111
...,000 analysis?GenomeMed2: 84. doi: 10.1186/gm205. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, et al. 2009. Sequence and structural variation in a human uncovered by short-read, massively parallel ligation sequencing using two-base encoding.Genome...
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Resource: Detecting copy number variation with mated short reads
- Paul Medvedev,
- Marc Fiume,
- Misko Dzamba,
- Tim Smith,
- and Michael Brudno
Genome Res. November 2010 20: 1613-1622; Published in Advance August 30, 2010, doi:10.1101/gr.106344.110
..., Paul Brudno T Smith Medvedev 10.1101/gr.106344.110 1088-9051 genome;gr.106344.110 Detecting copy number variation with mated short reads Resource Detecting copy number variation with mated short reads Paul Medvedev,1 Marc Fiume,1 Misko Dzamba,1 Tim Smith,1 and Michael Brudno1,2,3 1Department...
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Resource: Accurate detection and genotyping of SNPs utilizing population sequencing data
- Vikas Bansal,
- Olivier Harismendy,
- Ryan Tewhey,
- Sarah S. Murray,
- Nicholas J. Schork,
- Eric J. Topol,
- and Kelly A. Frazer
Genome Res. April 2010 20: 537-545; Published in Advance February 11, 2010, doi:10.1101/gr.100040.109
...sequence. A variety of tools have been developed that can efficiently align hundreds of millions of short reads to a reference sequence even in the presence of multiple errors in the reads (Li et al. 2008; Langmead et al. 2009; Li andDurbin 2009; Li et al. 2009b). Each base mismatch in an aligned read...
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Letter: Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes
- David L. Goode,
- Gregory M. Cooper,
- Jeremy Schmutz,
- Mark Dickson,
- Eidelyn Gonzales,
- Ming Tsai,
- Kalpana Karra,
- Eugene Davydov,
- Serafim Batzoglou,
- Richard M. Myers,
- and Arend Sidow
Genome Res. March 2010 20: 301-310; Published in Advance January 12, 2010, doi:10.1101/gr.102210.109
...functional variants. We resequenced 575 amplicons within 432 individuals at genomic sites enriched for evolutionary constraint and also analyzed variation within three published human genomes. We find that single-site measures of evolutionary constraint derived from mammalian multiple sequence alignments...
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Method: A comprehensively molecular haplotype-resolved genome of a European individual
- Eun-Kyung Suk,
- Gayle K. McEwen,
- Jorge Duitama,
- Katja Nowick,
- Sabrina Schulz,
- Stefanie Palczewski,
- Stefan Schreiber,
- Dustin T. Holloway,
- Stephen McLaughlin,
- Heather Peckham,
- Clarence Lee,
- Thomas Huebsch,
- and Margret R. Hoehe
Genome Res. October 2011 21: 1672-1685; Published in Advance August 3, 2011, doi:10.1101/gr.125047.111
...sequences of an individual genome is essential to relate genetic variation to genome function, phenotype, and disease. To address the importance of phase, we have generated the most complete haplotype-resolved genome to date, “Max Planck One” (MP1), by fosmid pool-based next generation sequencing. Virtually...
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Method: A reduced representation approach to population genetic analyses and applications to human evolution
- Francesca Luca,
- Richard R. Hudson,
- David B. Witonsky,
- and Anna Di Rienzo
Genome Res. July 2011 21: 1087-1098; Published in Advance May 31, 2011, doi:10.1101/gr.119792.110
..., University of Chicago, Chicago, Illinois 60637, USA; 2Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA Abstract Second-generation sequencing technologies allow surveys of sequence variation on an unprecedented scale. However, despite the rapid...
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Research: Alu repeat discovery and characterization within human genomes
- Fereydoun Hormozdiari,
- Can Alkan,
- Mario Ventura,
- Iman Hajirasouliha,
- Maika Malig,
- Faraz Hach,
- Deniz Yorukoglu,
- Phuong Dao,
- Marzieh Bakhshi,
- S. Cenk Sahinalp,
- and Evan E. Eichler
Genome Res. June 2011 21: 840-849; Published in Advance December 3, 2010, doi:10.1101/gr.115956.110
..., massively parallel ligation sequencing using two-base encoding.Genome Res 19: 1527–1541. Mills RE, Bennett EA, Iskow RC, Devine SE. 2007. Which transposable elements are active in the human ? Trends Genet 23: 183–191. Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S, Lee S, Suh D, Hong D, Kang HP, et al...

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