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Method: Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations
- David J. Witherspoon,
- Yuhua Zhang,
- Jinchuan Xing,
- W. Scott Watkins,
- Hongseok Ha,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. July 2013 23: 1170-1181; Published in Advance April 18, 2013, doi:10.1101/gr.148973.112
.... There is a significant dearth of exon-interrupting insertions among common Alu polymorphisms, but the density of singleton Alu insertions is constant across exonic and nonexonic regions. In one case, a validated novel singleton Alu interrupts a protein-coding exon of FAM187B . This implies that exonic Alu...
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Resource: Simultaneous structural variation discovery among multiple paired-end sequenced genomes
- Fereydoun Hormozdiari,
- Iman Hajirasouliha,
- Andrew McPherson,
- Evan E. Eichler,
- and S. Cenk Sahinalp
Genome Res. December 2011 21: 2203-2212; Published in Advance November 2, 2011, doi:10.1101/gr.120501.111
...&M approach, we proceeded as follows: • The ISV step:We analyzed each independently, using VariationHunter (Hormozdiari et al. 2009) for deletions and extended VariationHunter for Alu insertions (Hormozdiari et al. 2010).11 • The M step: To identify common structural variation among different s, we compared...
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Article: Diverse cis factors controlling Alu retrotransposition: What causes Alu elements to die?
- Matthew S. Comeaux,
- Astrid M. Roy-Engel,
- Dale J. Hedges,
- and Prescott L. Deininger
Genome Res. April 2009 19: 545-555; Published in Advance March 9, 2009, doi:10.1101/gr.089789.108
...to the divergence of the old and new world monkeys ( Shen et al. 1991 ; Lander et al. 2001 ; Batzer and Deininger 2002 ). Activity of the old Alu J/S subfamilies declined while being replaced by the younger Y subfamily (∼100,000 copies) ( Shen et al. 1991 ). Subsets of the Y subfamilies are the only known Alu...
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LETTER: Differential Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages
- Dale J. Hedges,
- Pauline A. Callinan,
- Richard Cordaux,
- Jinchuan Xing,
- Erin Barnes,
- and Mark A. Batzer
Genome Res. June 2004 14: 1068-1075; doi:10.1101/gr.2530404
...uninserted locus among the tested species indicates that this long-term maintenance of a duplication polymorphism is no more probable than that of a long-lived Alu insertion polymorphism. However, when considered together, these alternative pathways to the same observed state makes the observed insertion...
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Method: Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II
- Paul J. Norman,
- Steven J. Norberg,
- Lisbeth A. Guethlein,
- Neda Nemat-Gorgani,
- Thomas Royce,
- Emily E. Wroblewski,
- Tamsen Dunn,
- Tobias Mann,
- Claudia Alicata,
- Jill A. Hollenbach,
- Weihua Chang,
- Melissa Shults Won,
- Kevin L. Gunderson,
- Laurent Abi-Rached,
- Mostafa Ronaghi,
- and Peter Parham
Genome Res. May 2017 27: 813-823; Published in Advance March 30, 2017, doi:10.1101/gr.213538.116
...and 60%–80% of the world population, as assessed by HLA class I and II allele frequency (Norman et al. 2015). Also included in the analysis was one chimpanzee B cell line, derived from Clint (Yerkes pedigree number C0471), a chimpanzee of the Pan troglodytes verus (Western chimpanzee) subspecies, who...
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LETTER: Patterns of Human Diversity, within and among Continents, Inferred from Biallelic DNA Polymorphisms
- Chiara Romualdi,
- David Balding,
- Ivane S. Nasidze,
- Gregory Risch,
- Myles Robichaux,
- Stephen T. Sherry,
- Mark Stoneking,
- Mark A. Batzer,
- and Guido Barbujani
Genome Res. April 1, 2002 12: 602-612; doi:10.1101/gr.214902
..., most Alu loci of this study display what can be considered “normal” levels of interpopulation diversity. View this table: In this window In a new window Table 1. Alu Insertion Frequencies at 21 Alu Loci and Overall Standardized Genetic Variance Among Populations, Fst Genetic Differences among...
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LETTER: Whole-genome analysis of Alu repeat elements reveals complex evolutionary history
- Alkes L. Price,
- Eleazar Eskin,
- and Pavel A. Pevzner
Genome Res. November 2004 14: 2245-2252; doi:10.1101/gr.2693004
.... Genetic variation among world populations: Inferences from 100 Alu insertion polymorphisms. Genome Res. 13 : 1607 -1618. ↵ Willard, C., Nguyen, H.T., and Schmid, C.W. 1987 . Existence of at least three distinct Alu subfamilies. J. Mol. Biol. 26 : 180 -186. WEB SITE REFERENCES ↵ http...
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Letter: Mobile elements create structural variation: Analysis of a complete human genome
- Jinchuan Xing,
- Yuhua Zhang,
- Kyudong Han,
- Abdel Halim Salem,
- Shurjo K. Sen,
- Chad D. Huff,
- Qiong Zhou,
- Ewen F. Kirkness,
- Samuel Levy,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. September 2009 19: 1516-1526; Published in Advance May 13, 2009, doi:10.1101/gr.091827.109
..., the events present only in the HuRef or present in all five human samples may still be polymorphic among human populations. To further assess the human genomic diversity associated with polymorphic insertions, we tested 50 confirmed Alu insertions on a population panel composed of 15 European individuals...
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LETTER: AluInsertion Polymorphisms and Human Evolution: Evidence for a Larger Population Size in Africa
- Mark Stoneking,
- Jennifer J. Fontius,
- Stephanie L. Clifford,
- Himla Soodyall,
- Santosh S. Arcot,
- Nilmani Saha,
- Trefor Jenkins,
- Mohammad A. Tahir,
- Prescott L. Deininger,
- and Mark A. Batzer
Genome Res. November 1, 1997 7: 1061-1071; doi:10.1101/gr.7.11.1061
....M. , Smith M.T. , Bilsborough A. ( 1993 ) Amerindians and the price of modernization. in Urban ecology and health in the third world , eds Schell L.M. , Smith M.T. , Bilsborough A. ( Cambridge University Press , Cambridge, UK ), pp 221 – 243 . Alu Insertion Polymorphisms and Human Evolution: Evidence...
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LETTER: Genetic Evidence on the Origins of Indian Caste Populations
- Michael Bamshad,
- Toomas Kivisild,
- W. Scott Watkins,
- Mary E. Dixon,
- Chris E. Ricker,
- Baskara B. Rao,
- J. Mastan Naidu,
- B.V. Ravi Prasad,
- P. Govinda Reddy,
- Arani Rasanayagam,
- Surinder S. Papiha,
- Richard Villems,
- Alan J. Redd,
- Michael F. Hammer,
- Son V. Nguyen,
- Marion L. Carroll,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. June 1, 2001 11: 994-1004; Published in Advance May 8, 2001, doi:10.1101/gr.173301
...-chromosome (5 short-tandem repeats [STRs] and 20 biallelic polymorphisms), and autosomal (1 LINE-1 and 39 Alu inserts) variation in ∼265 males from eight different Telugu-speaking caste populations from the state of Andhra Pradesh in South India ( Bamshad et al. 1998 ). Comparisons were made to ∼400 individuals...

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