Sequencing methods for genotyping have moved from the research laboratory into the clinical laboratory. Sequencing is an assay format of choice for very high-complexity genotyping, especially when hundreds or thousands of bases of genetic sequence are analyzed. Clinical and Laboratory Standards Institute document MM09-A2-Nucleic Acid Sequencing Methods in Diagnostic Laboratory Medicine; Approved Guideline-Second Edition addresses diagnostic sequencing using both automated capillary electrophoresis sequencers and massively parallel sequencing instruments. Topics covered include specimen collection and handling; isolation and extraction of nucleic acid; template preparation; sequence generation, alignment, and assembly; validation and verification; ongoing QA; and reporting results.