Length and repeat-sequence variation in 58 STRs and 94 SNPs in two Spanish populations

• Published in: Forensic science international : genetics Vol. 30; pp. 66 - 70
• Main Authors: Casals, Ferran, Anglada, Roger, Bonet, Núria, Rasal, Raquel, van der Gaag, Kristiaan J., Hoogenboom, Jerry, Solé-Morata, Neus, Comas, David, Calafell, Francesc
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.09.2017; Elsevier
• Subjects: Alleles; Catalans; Chromosomes, Human, X; Chromosomes, Human, Y; Ethnic Groups - genetics; Female; Genetics, Population; High-Throughput Nucleotide Sequencing; Humans; Male; Massive parallel sequencing; Microsatellite Repeats; Pathology; Polymorphism, Single Nucleotide; Repeat sequence-based alleles; Roma; Spain; Massive parallel sequencing; Catalans; Roma; Repeat sequence-based alleles
• ISSN: 1872-4973; 1878-0326; 1878-0326
• DOI: 10.1016/j.fsigen.2017.06.006

•We genotyped the Illumina ForenSeq™ Primer Mix A in 88 Spanish Roma and 143 Catalans.•The repeat region sequence is much more informative than allele length for many loci.•Overall informativeness is extremely high.•A systematic yet concise nomenclature for sequence-based alleles is needed. We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in 88 Spanish Roma (Gypsy) samples and 143 Catalans. Since this platform is based in massive parallel sequencing, we have used simple R scripts to uncover the sequence variation in the repeat region. Thus, we have found, across 58 STRs, 541 length-based alleles, which, after considering repeat-sequence variation, became 804 different alleles. All loci in both populations were in Hardy-Weinberg equilibrium. FST between both populations was 0.0178 for autosomal SNPs, 0.0146 for autosomal STRs, 0.0101 for X-STRs and 0.1866 for Y-STRs. Combined a priori statistics showed quite large; for instance, pooling all the autosomal loci, the a priori probabilities of discriminating a suspect become 1−(2.3×10−70) and 1−(5.9×10−73), for Roma and Catalans respectively, and the chances of excluding a false father in a trio are 1−(2.6×10−20) and 1−(2.0×10−21).