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YSEQ

From ISOGG Wiki

YSEQ is a company established by Thomas and Astrid Krahn in November 2013 to make traditional Sanger sequencing products for the Y-chromosome available direct to consumer (DTC). The company also offers whole genome sequencing and mtDNA testing.

Team

  • Thomas Krahn, MSc (Dipl.-Ing.), CEO, product development
  • Astrid Krahn, Lab / customer service

Y-DNA testing

Y-SNPs

YSEQ offers a potentially unlimited menu of single SNPs to order (Wish a SNP). As of March 2016 they charge $17.50 per SNP and offer over 23,000 SNPs with primers, 33 Haplogroup Panels and 72 custom SNP panels .

Y-STRs

109 Y-STRs and 4 Y-STR panels can be ordered. Y-GATA-H4 is in the NIST Standard (-1 for FTDNA), DYS442 is in the FTDNA nomenclature [1]:

  • YSEQ-Alpha (18, overlap with the first 18 FTDNA markers) $58
  • YSEQ-Beta (17, overlap with FTDNA markers 19-37) $58
  • YSEQ-Alpha-Beta (37, overlap with FTDNA Y37 markers) $85
  • YSEQ-XTD (DYS464 palindromic panel including DYS464X and DYF399X) $25

Whole genome testing

In January 2017, YSEQ introduced whole-genome tests for direct-to-consumer purchase. These currently include coverage densities of 15x (approximately 45Gbases raw data per sample); 30x (~90Gbases); and 50x (~150Gbases). These tests require a new sample regardless of whether one is already on file with the company. The sample kit includes four cheek swabs rather than the normal two.

YSEQ extracts the DNA in-house and performs a quality control test to assure the sample meets acceptable tolerance levels of bacterial contamination. If the levels are too high, the tester will have the option to proceed with possible lower density coverage, or to provide a fresh sample. The actual NGS testing is performed by a third-party German laboratory using the Illumina NovaSeq 6000 Sequencing System. Data includes complete Y-chromosome (for males) and mitochondrial DNA sequencing. The raw-data FastQ files are then returned to YSEQ for analysis.

The analysis includes mtDNA HVR1/HVR2 and the coding region, and assignment to the deepest-identified haplogroup. For male testers, all Y-chromosome SNPs identified in Ybrowse are annotated to a VCF file with their ancestral and derived states. Separate files are generated for derived SNPs, and for novel SNP candidates and the InDel (insertion/deletion) mutations. Optionally, up to 10 novel SNPs can be verified by Sanger sequencing.

All resulting files (e.g., raw data FastQ, VCF) are available for download; an additional option can have the files mailed on a micro SD card. Note that for 2018 YSEQ has updated the reference coordinate system used from hg19/GRCh37 to Human Genome Version 38 (hg38; Genome Reference Consortium GRCh38) for all DNA tests.

As of July 2018 pricing for the YSEQ Whole Genome NGS testing was US$740 for the 15x coverage test, US$1,340 for the 30x test, and US$2,170 for the 50x test. An optional 10 Y-SNP Sanger sequencing run was US$100.

For further information see the product page on the company website.

Kit

Contains 2 swabs, each in a pouch containing one brush on a stick. Instructions for collecting DNA samples are included and available online (FAQ section). The brush needs to be dried, which is a simple preservation method. The stick is only for easy sample collection and can be trimmed short for easier sending back of the pouches. The kit weight is very low so the shipping is easy.

Blog posts

Resources

External links

References

  1. EMail Astrid Krahn, Alpha-Beta STR Y-GATA-H4 DYS442, 13 October 2015