Journal Article

A new 39-plex analysis method for SNPs including 15 blood group loci

Doi, Yusuke, Yamamoto, Yuji, Ishikawa, Takaki, Imabayashi, Kiyomi, Inagaki, Sachiyo, Yoshitome, Kei, Miyaishi, Satoru, Takata, Tomoyo, Ishizu, Hideo

2004

Overview

A novel 39-plex typing system for single nucleotide polymorphisms (SNPs) has been developed. This multiplex approach has the advantage of being able to type 38 autosomal SNPs and one sex-discriminating base exchange site on the X and Y chromosomes rapidly and simultaneously. The SNP loci on the autosomes, which we examined, contain 15 loci distributed on blood type genes: three on RhCE, two each on Km and Gc, and one each on Duffy, AcP1, Tf, MN, GPT, EsD, PI, and Kidd genes. Thirty-seven genomic DNA fragments containing a total of 38 SNPs and one sex-discriminating site were amplified in one multiplex PCR reaction. Following the reaction, single nucleotide primer extension reaction was performed by dividing these SNP loci into five groups. The SNP type of each of the 39 loci was determined at one time by capillary electrophoresis using the newly designed multi-injection method. The combined PD (power of discrimination) of this typing system was (1–1.1)×10 −14, and the MEC (mean exclusion chance) was 0.9990. We applied this system to forensic cases, including 16 paternity testing cases (13 non-exclusion and three exclusion cases) and one personal identification case. For the paternity testing cases, the highest Essen–Möller’s W-value was 0.9999995. The pM (matching probability) of the personal identification case was 2.22×10 −17. These data showed that this system was an excellent tool for use in forensic cases of paternity testing and personal identification.

• Publisher: Elsevier Ireland Ltd,Elsevier,The Lancet Publishing Group, a division of Elsevier Science Ltd,Elsevier Limited
• Subject: Analysis / Biological and medical sciences / Blood Group Antigens - genetics / Blood group loci / Blood groups / DNA Fingerprinting - methods / DNA Primers / Electrophoresis, Capillary / Female / Forensic genetics / Forensic sciences / Fundamental and applied biological sciences. Psychology / Gene Frequency / Genes / Genes. Genome / Genetics / Genomics / Humans / Identification / Investigative techniques, diagnostic techniques (general aspects) / Male / Medical sciences / Methods / Microbiology / Molecular and cellular biology / Molecular genetics / Mutation / Paternity / Paternity testing / Personal identification / Polymerase Chain Reaction / Polymorphism, Single Nucleotide / Power of discrimination / Sequence Analysis, DNA / Single nucleotide polymorphisms / Single nucleotide primer extension / Tandem Repeat Sequences