Evaluating probabilistic genotyping for low-pass DNA sequencing

Mandape, Sammed N.; Kapema, Kapema Bupe; Duque, Tiffany; Smuts, Amy; King, Jonathan L.; Crysup, Benjamin; Ge, Jianye; Budowle, Bruce; Woerner, August E.

doi:10.1016/j.fsigss.2022.10.001

Cited by 1 publication

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“…Because of its increased sensitivity of detection compared with microarrays and CE, NGS allows for dense SNP analyses on low-quantity and low-quality DNA samples [ 8 – 10 , 45 ]. Recently, there have been studies demonstrating that targeted SNP panels (5-10 K SNPs; termed herein as large SNP panels) can provide kinship associations up to 4th degree (and with some degree of accuracy at the 5th degree) relatives [ 24 , 25 ].…”

Section: Introductionmentioning

confidence: 99%

A cost–benefit analysis for use of large SNP panels and high throughput typing for forensic investigative genetic genealogy

2023

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Next-generation sequencing (NGS), also known as massively sequencing, enables large dense SNP panel analyses which generate the genetic component of forensic investigative genetic genealogy (FIGG). While the costs of implementing large SNP panel analyses into the laboratory system may seem high and daunting, the benefits of the technology may more than justify the investment. To determine if an infrastructural investment in public laboratories and using large SNP panel analyses would reap substantial benefits to society, a cost–benefit analysis (CBA) was performed. This CBA applied the logic that an increase of DNA profile uploads to a DNA database due to a sheer increase in number of markers and a greater sensitivity of detection afforded with NGS and a higher hit/association rate due to large SNP/kinship resolution and genealogy will increase investigative leads, will be more effective for identifying recidivists which in turn reduces future victims of crime, and will bring greater safety and security to communities. Analyses were performed for worst case/best case scenarios as well as by simulation sampling the range spaces with multiple input values simultaneously to generate best estimate summary statistics. This study shows that the benefits, both tangible and intangible, over the lifetime of an advanced database system would be huge and can be projected to be for less than $1 billion per year (over a 10-year period) investment can reap on average > $4.8 billion in tangible and intangible cost-benefits per year. More importantly, on average > 50,000 individuals need not become victims if FIGG were employed, assuming investigative associations generated were acted upon. The benefit to society is immense making the laboratory investment a nominal cost. The benefits likely are underestimated herein. There is latitude in the estimated costs, and even if they were doubled or tripled, there would still be substantial benefits gained with a FIGG-based approach. While the data used in this CBA are US centric (primarily because data were readily accessible), the model is generalizable and could be used by other jurisdictions to perform relevant and representative CBAs.

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