> For the complete documentation index, see [llms.txt](https://docs.nationalism.io/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.nationalism.io/ancestral-group-verification-process/genetic-testing/genetic-data-collection-methods.md). # Genetic data collection methods The following methods actually produce the raw genetic data that all the later ancestry or kinship analyses depend on. These are the lab techniques that measure DNA and turn a biological sample into usable genetic markers or sequences. ## **Autosomal single nucleotide polymorphism (SNP) genotyping** A lab method that measures a predefined set of common SNPs across the autosomal genome, often plus sex chromosomes and sometimes mtDNA markers. It directly produces the genotype calls at hundreds of thousands to millions of selected positions in the genome. It is very efficient for broad and moderate-resolution ancestry inference however it only tests selected markers, not the full genome. **What it enables:** * PCA * Admixture analysis * Relative matching * IBD detection * Local ancestry inference * Allele-frequency comparisons * Some haplotype methods **Example consumer services** * - $30 * - $49-$59 * - $79 * - $89 * - $99 ## **Whole-genome sequencing (WGS)** A sequencing method that reads most or nearly all of the DNA sequence across the genome. It directly produces sequence-level information from the person’s genome. Instead of only reading chosen SNPs, WGS attempts to determine the actual base sequence across nearly the whole genome. It is the most comprehensive general-purpose data source for ancestry analysis. WGS is ideal for highest overall resolution however it is expensive, more data-heavy and more computationally demanding. **What it enables:** Everything SNP genotyping enables, often better, plus: * Rare-variant analysis * Better haplotype analysis * Denser local ancestry inference * Structural variant analysis * More complete Y/mtDNA recovery * Better imputation reference use * Deeper research-grade analyses **Example consumer services** * - $399-$799 * - $245-$1295 * - $787 ## **Whole-exome sequencing (WES)** A sequencing method that reads mainly the exons, the protein-coding portions of genes. It directly generates sequence data from a defined subset of the genome. It could be used for ancestry analysis because it contains many variants, but it was designed mainly for medical genetics, not ancestry. It is more detailed than sparse marker sets in coding regions however it is poorly distributed for ancestry work because it ignores most of the genome and introduces uneven sampling. **What it enables:** * Some population structure analysis * Some kinship inference * Some ancestry estimation ## **Short tandem repeat (STR) testing** A method that measures the number of repeats at specific short tandem repeat loci. A lab will directly measure repeat lengths at selected genomic markers and outputs an STR profile. STRs mutate relatively quickly and are highly variable, which makes them very useful for forensic identification, paternity testing, close kinship analysis and some Y-lineage work. It is very strong for recent kinship and identity matching but it is less useful than genome-wide SNP or WGS data for broad ancestry inference. **What it enables** * Parentage testing * Forensic matching * Close relative comparison * Y-STR paternal lineage comparisons ## **Y-chromosome testing** A method focused on the Y chromosome, often using Y-SNPs, Y-STRs or or full Y sequencing. It directly measures markers or sequence on the Y chromosome and produces paternal-line genetic data. The Y chromosome is passed along the paternal line with limited recombination, making it useful for tracing one direct male lineage. It is very informative for one paternal line however it is only relevant to individuals with a Y chromosome, and only for one ancestral pathway. **What it enables** * Paternal haplogroup assignment * Direct paternal-line comparisons * Surname/paternal lineage studies in some contexts * Phylogenetic placement of male lineages **Example consumer services** * - $119-$449 ## **Mitochondrial DNA testing** A method focused on sequencing or genotyping mitochondrial DNA. It directly measures variants in mtDNA and produces maternal-line genetic data. mtDNA is inherited maternally, so it can trace one direct maternal line across deep time. Useful for one maternal line and deep maternal ancestry, but similar to Y-DNA, it only represents one ancestral line out of many. **What it enables** * Maternal haplogroup assignment * Direct maternal-line comparison * Lineage phylogeny **Example consumer services** * - $159 ## Most suitable genetic methods **Population testing** Autosomal SNP genotyping is the most suitable for broad population testing for things like ancestry. It is cheaper and can be more easily scaled to be used across a large population. Whole-genome sequencing is also potentially suitable, however the problems of the cost and time required to sequence people's genome at population scale makes it more difficult to recommend as a solution. A combination approach might do whole-genome sequencing on people who have larger amounts of evidence about their ancestral background. These individuals might be suitable candidates to become part of a reference panel if their historical lineage can be more easily proven. If the priority is to have a higher confidence and high resolution outcome then a WGS approach will be the most suitable choice. If a cost effective and more easily scalable solution is a pragmatic requirement then autosomal SNP genotyping is the most suitable choice. **Direct lineage testing** STR, Y-chromosome and mitochondrial DNA testing are all suitable methods for looking at direct ancestry and lineage. Whole-genome sequencing is also useful for adding a greater depth of information that can strengthen any subsequent analytical approaches.