Development of a Multiplex Single Base Extension Assay for Mitochondrial DNA Haplogroup Typing

Overview

Journal Croat Med J

Specialty General Medicine

Date 2007 Aug 19

PMID 17696300

Citations 6

Authors

Tahnee M Nelson

Rebecca S Just

Odile Loreille

Moses S Schanfield

Daniele Podini

Affiliations

Soon will be listed here.

Abstract

Aim: To provide a screening tool to reduce time and sample consumption when attempting mitochondrial DNA (mtDNA) haplogroup typing.

Methods: A single base primer extension assay was developed to enable typing, in a single reaction, of twelve mtDNA haplogroup specific polymorphisms. For validation purposes a total of 147 samples were tested including 73 samples successfully haplogroup typed using mtDNA control region (CR) sequence data, 20 samples inconclusively haplogroup typed by CR sequence data, 21 samples previously haplogroup typed using RFLP analysis, and 31 samples of known ancestral origin without previous haplogroup typing. Additionally, two highly degraded human bones embalmed and buried in the early 1950s were analyzed using the SNP multiplex.

Results: When the SNP multiplex was used to type the 96 previously CR sequenced specimens, an increase in haplogroup or macrohaplogroup assignment relative to conventional CR sequence analysis was observed. The single base extension assay was also successfully used to assign a haplogroup to decades-old, embalmed skeletal remains dating to World War II.

Conclusion: The SNP multiplex was successfully used to obtain haplogroup status of highly degraded human bones, and demonstrated the ability to eliminate possible contributors. The SNP multiplex provides a low-cost, high throughput method for typing of mtDNA haplogroups A, B, C, D, E, F, G, H, L1/L2, L3, M, and N that could be useful for screening purposes for human identification efforts and anthropological studies.

Citing Articles

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Validation of 58 autosomal individual identification SNPs in three Chinese populations.

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mtDNA Mutations and Their Role in Aging, Diseases and Forensic Sciences.

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Using multiplex single-base extension typing to screen for mutants defective in RNA editing.

Takenaka M, Brennicke A Nat Protoc. 2012; 7(11):1931-45.

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Multiplex analysis of mitochondrial DNA pathogenic and polymorphic sequence variants.

Poole J, Procaccio V, Brandon M, Merrick G, Wallace D Biol Chem. 2010; 391(10):1115-30.

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