SNP Trace™ Panel

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Publication protocol

STR and SNP genotyping: STR profiling to examine the core set of loci used for cell line authentication22 was performed using the AmpFLSTR® Identifiler® kit, with a reduced volume modification of the manufacturer's instructions (Applied Biosystems, ThermoFisher Scientific; catalogue number 4322288). Identifiler® data were obtained using an ABI 3730 genetic analyzer and analyzed using GeneMapper 4.0 software (Applied Biosystems, ThermoFisher Scientific). Percent match comparisons were made using the Tanabe algorithm23, 24; a step‐by‐step workflow for profile comparison is set out in the Supporting Information Methods. X‐Chromosome‐specific STR loci were analyzed using a DXS multiplex PCR, developed at the DSMZ. A detailed procedure for the DXS multiplex PCR is set out in the Supporting Information Methods. Control samples were included for comparison from the male cell line CAKI‐2, and the female cell line A‐204 (Supporting Information Table S3).
Y‐Chromosome‐specific STR loci and autosomal STR loci were analyzed using PowerPlex® Y23 and PowerPlex® Fusion 6C Systems (Promega, Madison, WI), in accordance with the manufacturer's instructions.25, 26 Data were analyzed using GeneMapper ID‐X v1.4.
SNP analysis was performed using the Fluidigm SNP Trace™ Panel (Fluidigm, South San Francisco, CA; catalogue number 100–6,280) as previously reported.16 Percent match comparisons used the same workflow employed for STR profiling. Allele calls for sex‐specific SNP loci were confirmed by direct PCR amplification and sequencing of the relevant loci as described in the Supporting Information Methods.
Locations of all Y‐STR and Y‐SNP loci evaluated in the current study are shown in Supporting Information Figure S1.

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