Development and optimisation of five multiplex assays with 115 of the AIM SNPs from the EUROFORGEN AIMs set on the Sequenom® MassARRAY® system

TY - GEN

T1 - Development and optimisation of five multiplex assays with 115 of the AIM SNPs from the EUROFORGEN AIMs set on the Sequenom® MassARRAY® system

AU - Lundsberg, Birgitte Møller

AU - Johansen, Peter

AU - Børsting, Claus

AU - Morling, Niels

PY - 2013/11/1

Y1 - 2013/11/1

N2 - Ancestry informative markers (AIMs) can be used in forensic genetics to infer the biogeographic ancestry of a person, e.g. from a DNA trace sample found at a crime scene. The European Forensic Genetics Network of Excellence (EUROFORGEN-NOE) selected a panel of more than 200 AIM SNPs with the purpose of developing multiplex assays for forensic ancestry testing. The SNPs were selected to discriminate between five major population groups (Africans, Europeans, Asians, Native Americans and Pacific Islanders). Here, we describe the development of five PCR multiplexes for detection with the Sequenom MassARRAY® system of 115 AIM SNPs from the EUROFORGEN selection panel. The five multiplexes allowed typing of 25, 33, 24, 13 and 29 AIM SNPs, respectively. Furthermore, one X and two Y chromosome SNP were included for sex determination. We evaluated the sensitivity and overall performance of each multiplex in a Danish population. The SNP call rates were 93.1%, 96.1%, 97.3%, 97.2%, and 97.1% for the five multiplexes, respectively. The typing results were robust when more than 1.25ng DNA was used in the PCR. The data analysis was performed using a custom made script in the statistical software R. This script called the phenotypes automatically by using information on peak heights, signal to noise ratios and allelic balances. Three SNPs were sequenced to elucidate skewed allelic balances. These results as well as the allelic frequencies for all SNPs will be presented.

AB - Ancestry informative markers (AIMs) can be used in forensic genetics to infer the biogeographic ancestry of a person, e.g. from a DNA trace sample found at a crime scene. The European Forensic Genetics Network of Excellence (EUROFORGEN-NOE) selected a panel of more than 200 AIM SNPs with the purpose of developing multiplex assays for forensic ancestry testing. The SNPs were selected to discriminate between five major population groups (Africans, Europeans, Asians, Native Americans and Pacific Islanders). Here, we describe the development of five PCR multiplexes for detection with the Sequenom MassARRAY® system of 115 AIM SNPs from the EUROFORGEN selection panel. The five multiplexes allowed typing of 25, 33, 24, 13 and 29 AIM SNPs, respectively. Furthermore, one X and two Y chromosome SNP were included for sex determination. We evaluated the sensitivity and overall performance of each multiplex in a Danish population. The SNP call rates were 93.1%, 96.1%, 97.3%, 97.2%, and 97.1% for the five multiplexes, respectively. The typing results were robust when more than 1.25ng DNA was used in the PCR. The data analysis was performed using a custom made script in the statistical software R. This script called the phenotypes automatically by using information on peak heights, signal to noise ratios and allelic balances. Three SNPs were sequenced to elucidate skewed allelic balances. These results as well as the allelic frequencies for all SNPs will be presented.

M3 - Conference article

SN - 1875-1768

VL - 4

SP - e182-e183

JO - Forensic Science International: Genetics. Supplement Series

JF - Forensic Science International: Genetics. Supplement Series

IS - 1

T2 - 25’th congress of the International Society of Forensic Genetics

Y2 - 2 September 2013 through 7 September 2013

ER -