The Snipper 2.5

app suite

Excel format required

Forensic MPS AIMs Panel Reference Sets

The training sets provided for each forensic MPS ancestry panel have been constructed from the published SNP genotypes of 1000 Genomes (the 2020 high coverage variant calls); HGDP-CEPH, Simons Foundation and Estonian Genome Diversity Projects (SGDP and EGDP).
The ‘active’ worksheet in position 1 of each panel’s training set file contains a recommended standard reference dataset for use in Snipper, comprising 1000 Genomes (1KG) African YRI, European CEU, South Asian GIH, East Asian CHB genotypes, plus HGDP-CEPH Middle East, Oceanian and Native American genotypes. The VISAGE BT panel does not have Middle East genotypes in the reference dataset so it differentiates six population groups. The American data also include 18 1KG Peruvians from Lima (PEL) with no detected admixture. Rows 2-5 of this worksheet are not read by Snipper and contain genomic data for each SNP.
The other worksheets compile the remaining 1000 Genomes populations into unadmixed and admixed sets; HGDP-CEPH populations not used in the reference dataset; 130 SGDP samples; 402 EGDP samples - note some SNP data are missing from EGDP. Additional in-house population data are included for the VISAGE Basic Tool ancestry panel.
The Verogen ForenSeq DNA Signature Kit UAS software reports the allele from the opposite strand to the reference sequence in 18 of 56 SNPs, marked in blue. These inverse nucleotides have been applied to the original genotype data in all cases. Each SNP is in the Thermo Fisher Precision ID Ancestry panel with their unmodified reference strand genotypes.

Users can select and transpose sample rows from the other worksheets into the standard reference dataset to act as alternative/additional reference data (final column bears a ‘1’ label), or as test samples (final column bears a ‘0’ label). Cell A1 denotes the sample number and must be adjusted appropriately. Cell C1 denotes the number of populations in the training set and test samples are marked as belonging to one of the training set populations in column B.

With all of the above in mind, download new versions of VISAGE BT grid, TFS Precision ID 165 grid or Forenseq 56 grid. Then paste your profiles as extra rows ending in 0 into it, and modify the number of individuals in first leftmost cell accordingly. At this stage you will have a hybrid profile and training set file to analyse. Then go to the multiple profiles tool in Snipper and input the resulting file.