Multiplex PCR and minisequencing of SNPs—a model with 35 Y chromosome SNPs

Sánchez, Juan José Martínez; Børsting, Claus; Hallenberg, Charlotte; Buchard, Anders; Hernández, Alexis; Morling, Niels

doi:10.1016/s0379-0738(03)00299-8

Cited by 122 publications

(105 citation statements)

References 30 publications

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“…11 The markers P2, M22, M70, M75, M128, M168, M201, M207, M269 and M304 were also typed using singleplex PCR conditions. 4,11,12 For the marker V6, 10 we used the PCR primer sequences: V6F: 5 0 -CCTATAGAGTCCCTGTCCCTGA-3 0 , V6R: 5 0 -CTTGCTGCTGAGTGAGCTTCT-3 0 (0.4 mM of each primer). SBE primers not described by Sanchez et al 11 (0.2 mM of each primer) are given in Table 1.…”

Section: Biallelic Marker Typingmentioning

confidence: 99%

High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males

et al. 2005

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We genotyped 45 biallelic markers and 11 STR systems on the Y chromosome in 201 male Somalis. In addition, 65 sub-Saharan Western Africans, 59 Turks and 64 Iraqis were typed for the biallelic Y chromosome markers. In Somalis, 14 Y chromosome haplogroups were identified including E3b1 (77.6%) and K2 (10.4%). The haplogroup E3b1 with the rare DYS19-11 allele (also called the E3b1 cluster c) was found in 75.1% of male Somalis, and 70.6% of Somali Y chromosomes were E3b1, DYS19-11, DYS392-12, DYS437-14, DYS438-11 and DYS393-13. The haplotype diversity of eight Y-STRs ('minimal haplotype') was 0.9575 compared to an average of 0.9974 and 0.9996 in European and Asian populations. In sub-Saharan Western Africans, only four haplogroups were identified. The West African clade E3a was found in 89.2% of the samples and the haplogroup E3b1 was not observed. In Turks, 12 haplogroups were found including J2*(xJ2f2) (27.1%), R1b3*(xR1b3d, R1b3f) (20.3%), E3b3 and R1a1*(xR1a1b) (both 11.9%). In Iraqis, 12 haplogroups were identified including J2*(xJ2f2) (29.7%) and J*(xJ2) (26.6%). The data suggest that the male Somali population is a branch of the East African population -closely related to the Oromos in Ethiopia and North Kenya -with predominant E3b1 cluster c lineages that were introduced into the Somali population 4000 -5000 years ago, and that the Somali male population has approximately 15% Y chromosomes from Eurasia and approximately 5% from sub-Saharan Africa.

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Section: Biallelic Marker Typingmentioning

confidence: 99%

High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males

et al. 2005

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“…SNPs for individual, phenotypic, and species identification, as well as, ancestry and parentage analysis are available in cats and can be assayed by various techniques 9, 44, 45, 46, 47. Hence, this study embarked upon developing an effective SNP identification panel that can be easily adapted into forensic laboratories for use with cat evidence.…”

Section: Discussionmentioning

confidence: 99%

SNP Miniplexes for Individual Identification of Random‐Bred Domestic Cats

Brooks

Creighton

Gandolfi

et al. 2016

Journal of Forensic Sciences

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Phenotypic and genotypic characteristics of the cat can be obtained from single nucleotide polymorphisms (SNPs) analyses of fur. This study developed miniplexes using SNPs with high discriminating power for random‐bred domestic cats, focusing on individual and phenotypic identification. Seventy‐eight SNPs were investigated using a multiplex PCR followed by a fluorescently labeled single base extension (SBE) technique (SNaPshot®). The SNP miniplexes were evaluated for reliability, reproducibility, sensitivity, species specificity, detection limitations, and assignment accuracy. Six SNPplexes were developed containing 39 intergenic SNPs and 26 phenotypic SNPs, including a sex identification marker, ZFXY. The combined random match probability (cRMP) was 6.58 × 10−19 across all Western cat populations and the likelihood ratio was 1.52 × 1018. These SNPplexes can distinguish individual cats and their phenotypic traits, which could provide insight into crime reconstructions. A SNP database of 237 cats from 13 worldwide populations is now available for forensic applications.

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“…SNaPshot technology uses fluorescence detection and has been used for genotyping 3 SNPs of CYP2C9 (26 ). The approach uses SBE with fluorescently labeled ddNTPs followed by capillary gel electrophoresis for SNP genotyping and has been used for analysis of up to 35 SNPs simultaneously (27 ). In principle, the first step for SNP genotyping in the SNaPshot method, SBE for generation of allele-specific products, is the same as SPC-SBE.…”

Section: Discussionmentioning

confidence: 99%

Multiplex Genotyping of Cytochrome P450 Single-Nucleotide Polymorphisms by Use of MALDI-TOF Mass Spectrometry

2007

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Background: Polymorphisms in cytochrome P450 (CYP450) genes contribute to interindividual differences in the metabolism of xenobiotic chemicals, including the vast majority of drugs, and may lead to toxicity and adverse drug reactions. Studies on these polymorphisms in research and diagnostic settings typically involve large-scale genotyping and hence require highthroughput assays. Methods: We used the previously developed solidphase capture-single-base extension (SPC-SBE) approach for concurrent analysis of 40 single-nucleotide polymorphisms (SNPs) of CYP2C9 and 50 SNPs of CYP2A13, both genes belonging to the CYP450 family. Desired SNP-containing regions for each gene were amplified in a single-step multiplex PCR. We designed a library of primers to anneal immediately upstream of the selected SNPs and extended it with biotinylated terminators using PCR products as templates. Biotinylated extension products were isolated by affinity purification and analyzed with MALDI-TOF mass spectrometry to determine SNP genotypes. Results: We analyzed 11 samples for CYP2C9 and 14 samples for CYP2A13 with unambiguous detection of SNPs in all samples. Many samples showed a high occurrence of heterozygotes for both genes, with as many as 10 of 50 SNPs appearing as heterozygotes in 1 sample genotyped for CYP2A13. Conclusions: The SPC-SBE method provides an efficient means for genotyping SNPs from the CYP450

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Multiplex PCR and minisequencing of SNPs—a model with 35 Y chromosome SNPs

Cited by 122 publications

References 30 publications

High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males

High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males

SNP Miniplexes for Individual Identification of Random‐Bred Domestic Cats

Multiplex Genotyping of Cytochrome P450 Single-Nucleotide Polymorphisms by Use of MALDI-TOF Mass Spectrometry

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