Development and validation of a custom panel including 183 Y‐SNPs for Chinese Y‐chromosomal haplogroups dissection using a MALDI‐TOF MS system

Abstract

Y‐chromosome SNP haplogroups exhibit geographic structuring in many populations around the world. Therefore, Y‐chromosome haplogroups have been widely used to infer paternal biogeographical ancestry and high‐resolution paternal lineage classification. In the present study, we designed a customized panel containing 183 Y‐SNPs based on previous studies and evaluated the genotyping performance and repeatability, concordance, sensitivity, and ability of analysing case‐type samples using a MALDI‐TOF MS platform. The average call rate for duplicate typing of any one SNP in the panel was 97.0%. In the concordance and accuracy study, the results of haplogroup designation obtained from MALDI‐TOF MS platform were fully consistent with those obtained from the next‐generation sequencing (NGS) platform. The optimal amount of template DNA in the PCR seemed to be 10 ng. However, if less DNA (≥156.25 pg) was available, it was still possible to obtain meaningful haplogroup information. For the application part, this panel could be applied for the detection of blood, semen, and buccal swabs samples. Particularly, blood stain on FTA card samples could be dissected by direct PCR amplification on the MALDI‐TOF MS platform. Besides, 371 unrelated male individuals from four Chinese ethnic groups (Han, Hui, Mongolian, and Kazak) were detected using this panel. Total 78 terminal haplogroups were found and the haplogroup diversity was 0.933576. The results demonstrate that this panel could be an accurate, fast, and cost‐effective method for database construction where the amount of sample material is less of a concern and when the cost of the assay is taken into consideration.

The relationship between LRP5 rs556442 and rs638051 polymorphisms and mutations and their influence on bone metabolism in postmenopausal Xinjiang women with type 2 diabetes

“…Resin (Xingruikebo, Shihezi, China) purification procedure was also performed using the mass array nanodispenser RS1000 spotter (Sequenom), and the extension product was moved to the 384-pad spectral chip. [12][13][14] The MALDI-TOF MS (Sequenom) was performed to detect rs556442 and rs638051 genotypes under different conditions. 15 After the above reaction steps, the chip was put into the mass spectrometer (Sequenom).…”