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Spinocerebellar ataxia type 3/Machado–Joseph disease (SCA3/MJD) is a neurodegenerative disorder caused by the <i>ATXN3</i> CAG repeat expansion. Preimplantation genetic testing for monogenic disorders (PGT-M) of SCA3/MJD should include reliable repeat expansion detection coupled with high-risk allele determination using informative linked markers. One couple underwent SCA3/MJD PGT-M combining <i>ATXN3</i> (CAG)_n triplet-primed PCR (TP-PCR) with customized linkage-based risk allele genotyping on whole-genome-amplified trophectoderm cells. Microsatellites closely linked to <i>ATXN3</i> were identified and 16 markers were genotyped on 187 anonymous DNAs to verify their polymorphic information content. In the SCA3/MJD PGT-M case, the <i>ATXN3</i> (CAG)_n TP-PCR and linked marker analysis results concurred completely. Among the three unaffected embryos, a single embryo was transferred and successfully resulted in an unaffected live birth. A total of 139 microsatellites within 1 Mb upstream and downstream of the <i>ATXN3</i> CAG repeat were identified and 8 polymorphic markers from each side were successfully co-amplified in a single-tube reaction. A PGT-M assay involving <i>ATXN3</i> (CAG)_n TP-PCR and linkage-based risk allele identification has been developed for SCA3/MJD. A hexadecaplex panel of highly polymorphic microsatellites tightly linked to <i>ATXN3</i> has been developed for the rapid identification of informative markers in at-risk couples for use in the PGT-M of SCA3/MJD.