3 ms·

DNA microarrays do have limitations vs. RNAseq, but they are accurate and repeatable when used properly. https://en.wikipedia.org/wiki/DNA_microarray https://e

DNA microarrays do have limitations vs. RNAseq, but they are accurate and repeatable when used properly. https://en.wikipedia.org/wiki/DNA_microarray https://en.wikipedia.org/wiki/DNA_microarray Calling them 'super error prone' is simply inaccurate. There was a good 5-10 years where microarrays were the go-to method for genomic investigation. Since RNA-seq has supplanted it, there has been no revolution in overturning those old results. At best, RNA-seq reveals what microarrays cannot: novel sequences, specific sequences that have difficulty hybridizing, etc. The variation between these services is due primarily to how the data is interpreted and presented to customers, not the reads themselves.

nkrumm 8y ago
Note that these companies are not doing DNA microarrays in the sense you're describing (which is for quantifying gene expression by mRNA level). RNA-seq is (now) arguably better for this purpose as well (better dynamic range, primarily), but again this is not what any of the ancestry or personalized genetics companies are doing. In this case "SNP microarray" is a "digital" (or binary) readout of the genomic DNA sequence; specifically the array has attached to it sequences that match both the "reference allele" (e.g., a "G") and the "alternate allele" (e.g., "A" or some other base). Note that across the world's population, most sites in the human genome are "bi-allelic" meaning that there's really only two variants at each site, though of course it is possible to have tri-allelic or even fully polymorphic (A, T, C, or G) sites. For the purposes of ancestry, bi-allelic identification of commonly polymorphic sites is adequate, though the more sites and the rarer those sites are in world populations, the more specific you can be re: ancestry. This is why the gold standard for ancestry and haplotyping is whole genome sequencing-- you simply get far more informative sites to map to other populations.

nkrumm 8y ago

Note that these companies are not doing DNA microarrays in the sense you're describing (which is for quantifying gene expression by mRNA level). RNA-seq is (now) arguably better for this purpose as well (better dynamic range, primarily), but again this is not what any of the ancestry or personalized genetics companies are doing. In this case "SNP microarray" is a "digital" (or binary) readout of the genomic DNA sequence; specifically the array has attached to it sequences that match both the "reference allele" (e.g., a "G") and the "alternate allele" (e.g., "A" or some other base). Note that across the world's population, most sites in the human genome are "bi-allelic" meaning that there's really only two variants at each site, though of course it is possible to have tri-allelic or even fully polymorphic (A, T, C, or G) sites. For the purposes of ancestry, bi-allelic identification of commonly polymorphic sites is adequate, though the more sites and the rarer those sites are in world populations, the more specific you can be re: ancestry. This is why the gold standard for ancestry and haplotyping is whole genome sequencing-- you simply get far more informative sites to map to other populations.