A method for obtaining nucleic acid sequence information from a biological sample comprising: (a) providing a biological sample comprising different target nucleic acids, wherein each of the different target nucleic acids comprises, from 3' to 5': contiguous first, second, and third target domains; (b) contacting the biological sample with a plurality of different probe sets to form hybridization complexes with the different target nucleic acids, wherein each probe set comprises: (i) a first probe comprising, from 5' to 3': a first priming sequence and a sequence that is substantially complementary to a first target domain; and (ii) a second probe comprising, from 5' to 3': a sequence substantially complementary to a third target domain, and a second priming sequence, wherein the plurality of probe sets comprises a plurality of probes configured to selectively hybridize to polymorphic regions that are informative of the identity of the source of the sample; (c) contacting the hybridization complexes with an extension enzyme and nucleotides, wherein the first probes are extended along the second target domains of hybridization complexes formed in (b); (d) ligating the extended first probes to the second probes to form amplification templates; (e) amplifying the amplification templates with first and second primers that are complementary to the first priming sequence and the second priming sequence to produce amplicons, wherein there is no purification of the nucleic acid from the biological sample prior to the contacting step (b); (f) obtaining nucleic acid sequence information for a plurality of portions of the amplified sample, wherein the obtaining comprises detecting the amplicons on a nucleic acid array or comprises massively parallel sequencing; and (g) using the sequence information from step (f) to confirm the identity of the sample in a genetic testing assay. (a) providing a biological sample comprising different target nucleic acids, wherein each of the different target nucleic acids comprises, from 3' to 5': contiguous first, second, and third target domains; (b) contacting the biological sample with a plurality of different probe sets to form hybridization complexes with the different target nucleic acids, wherein each probe set comprises: (i) a first probe comprising, from 5' to 3': a first priming sequence and a sequence that is substantially complementary to a first target domain; and (ii) a second probe comprising, from 5' to 3': a sequence substantially complementary to a third target domain, and a second priming sequence, wherein the plurality of probe sets comprises a plurality of probes configured to selectively hybridize to polymorphic regions that are informative of the identity of the source of the sample; (c) contacting the hybridization complexes with an extension enzyme and nucleotides, wherein the first probes are extended along the second target domains of hybridization complexes formed in (b); (d) ligating the extended first probes to the second probes to form amplification templates; (e) amplifying the amplification templates with first and second primers that are complementary to the first priming sequence and the second priming sequence to produce amplicons, wherein there is no purification of the nucleic acid from the biological sample prior to the contacting step (b); (f) obtaining nucleic acid sequence information for a plurality of portions of the amplified sample, wherein the obtaining comprises detecting the amplicons on a nucleic acid array or comprises massively parallel sequencing; and (g) using the sequence information from step (f) to confirm the identity of the sample in a genetic testing assay.