Rapid Screening for Mitochondrial and Y-Chromosome Haplogroups in Routine DNA Analysis

GALA ZUCCARELLI, EVGUENIA ALECHINE, MARIELA CAPUTO, CECILIA BOBILLO, DANIEL CORACH AND ANDREA SALA

Berlin-Alemania

Workshop; 7th Y User Workshop / 4th EMPOP; 2010

Y-STR User workshop

The population of Argentina, as that of other South American countries, is the result of an intercontinental admixture. Recent results confirmed this observation. In order to refine the admixture levels a rapid screening approach has been developed for discerning the major haplogroup to which a sample might belong for either the maternal or paternal lineages. The analysis is part of the DNA typing required for paternity testing or criminal casework and is only conducted proving the participant sign an informed written consent statement in which they accept to participate in this research. After extraction, DNA is quantitated by means of Real Time PCR (Rt-PCR) using commercial kits (Plexor HY-Promega or Quantifiler-ABI, USA). Quantitated samples are then submitted to two multiplex Rt-PCRs in order to determine the major Native American mtDNA and Y-chromosome haplogroups by means of High Resolution Melting (HRM) analysis. In the first, a cocktail of primers flanking nucleotide  substitutions that define C mtDNA haplogroup and A2, B2, and D1 sub-haplogroups are used. The second include primers flanking Y-SNPs M242, M3, M269 and U179 that allow discriminating Q and non-Q Hgs. In all cases amplicons are less than 120 nucleotides long in order to increase the signal detection. This new working-flow strategy facilitates and speed-up the screening process that may lead to detailed sequencing analysis of particular samples, or for further molecular epidemiological investigations in which continental origin influences might be of relevance.