The use of polymorphic Alu insertions in human DNA fingerprinting

Novick, Gabriel E.; Gonzalez, Tatiana Pereira; Garrison, Jennifer L.; Novick, Corina C.; Batzer, Mark A.; Deininger, Prescott L.; Herrera, René J.

doi:10.1007/978-3-0348-8583-6_26

Cited by 17 publications

(13 citation statements)

References 23 publications

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“…Alu elements that are polymorphic for insertion presence/ absence have previously proven useful for the study of human population genetics and forensics (Perna et al, 1992;Novick et al, 1993;Batzer et al, 1994;Jorde et al, 2000;Watkins et al, 2001). Alu insertion polymorphisms are considered to be population-specific when the frequency of the Alu in one of the tested populations differs by 625 % from the Alu frequencies of the other populations tested.…”

Section: Discussionmentioning

confidence: 99%

The <i>Alu</i> Yc1 subfamily: sorting the wheat from the chaff

Garber

Hedges

Herke

et al. 2005

Cytogenet Genome Res

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Members of the Alu Yc1 subfamily are distinguished from the older Alu Y subfamily by a signature G→A substitution at base 148 of their 281-bp consensus sequence. Members of the much older and larger Alu Y subfamily could have by chance accumulated this signature G→A substitution and be misclassified as belonging to the Alu Yc1 subfamily. Using a Mahanalobis classification method, it was estimated that the “authentic” Alu Yc1 subfamily consists of approximately 262 members in the human genome. PCR amplification and further analysis was successfully completed on 225 of the Yc1 Alu family members. One hundred and seventy-seven Yc1 Alu elements were determined to be monomorphic (fixed for presence) in a panel of diverse human genomes. Forty-eight of the Yc1 Alu elements were polymorphic for insertion presence/absence in diverse human genomes. The insertion polymorphism rate of 21% in the human genome is similar to rates reported previously for other “young” Alu subfamilies. The polymorphic Yc1 Alu elements will be useful genetic loci for the study of human population genetics.

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Section: Discussionmentioning

confidence: 99%

The <i>Alu</i> Yc1 subfamily: sorting the wheat from the chaff

Garber

Hedges

Herke

et al. 2005

Cytogenet Genome Res

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“…The use of retrotransposon insertions as phylogenetic and population genetic markers has seen an increasing popularity in recent years (Okada 1991;Minghetti and Dugaiczyk 1993;Novick et al 1993;Batzer et al 1994;Stoneking et al 1997;Hamdi et al 1999;Nasidze et al 2001;Romualdi et al 2002;Salem et al 2003;Watkins et al 2003;Roos et al 2004;Shedlock et al 2004;Ray et al 2005;Schmitz et al 2005;Nikaido et al 2006;Witherspoon et al 2006;Herke et al 2007;Xing et al 2007a;Li et al 2009;Osterholz et al 2009;Nilsson et al 2010;Roos et al 2011;Suh et al 2011). Short interspersed elements (SINEs) are <500 bp in length and generate new copies of themselves through reverse transcription of an RNA intermediate into a new position in the genome (Luan et al 1993;Luan and Eickbush 1995;Cost et al 2002).…”

Section: Introductionmentioning

confidence: 99%

An Alu-Based Phylogeny of Gibbons (Hylobatidae)

Meyer

McLain

Oldenburg

et al. 2012

Molecular Biology and Evolution

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Gibbons (Hylobatidae) are small, arboreal apes indigenous to Southeast Asia that diverged from other apes 15-18 Ma. Extant lineages radiated rapidly 6-10 Ma and are organized into four genera (Hylobates, Hoolock, Symphalangus, and Nomascus) consisting of 12-19 species. The use of short interspersed elements (SINEs) as phylogenetic markers has seen recent popularity due to several desirable characteristics: the ancestral state of a locus is known to be the absence of an element, rare potentially homoplasious events are relatively easy to resolve, and samples can be quickly and inexpensively genotyped. During radiation of primates, one particular family of SINEs, the Alu family, has proliferated in primate genomes. Nomascus leucogenys (northern white-cheeked gibbon) sequences were analyzed for repetitive content with RepeatMasker using a custom library. The sequences containing Alu elements identified as members of a gibbon-specific subfamily were then compared with orthologous positions in other primate genomes. A primate phylogenetic panel consisting of 18 primate species, including 13 gibbon species representing all four extant genera, was assayed for all loci, and a total of 125 gibbon-specific Alu insertions were identified. The resulting amplification patterns were used to generate a phylogenetic tree. We demonstrate significant support for Symphalangus as the most basal lineage within the family. Our findings also place Nomascus as a derived lineage, sister to Hoolock, with the NomascusHoolock clade sister to Hylobates. Further, our analysis groups N. leucogenys and Nomascus siki as sister taxa to the exclusion of the other Nomascus species assayed. This study represents the first use of SINEs to determine the genus level phylogenetic relationships within the family Hylobatidae. These relationships have been resolved with robust support at most internal nodes, demonstrating the utility of SINE-based phylogenetic analysis. We postulate that hybridization and rapid radiation may have contributed to the complex and contradictory findings of the previous studies. Our findings will aid in the conservation of these threatened primates and inform future studies of the biogeographical history and distribution of modern gibbon species.

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“…Alu sequences). Some of these elements display a high degree of polymorphism at specific insertion sites (Perna et al, 1992;Novick et aL, 1993).…”

Section: Dna-level Variationmentioning

confidence: 99%