Supplementary info:

Genotyping of haplotype markers:

For the AC1 and D3S1287 reactions, primers flanking each marker were utilised in a standard 25
μl PCR reaction containing 1x GoTaq buffer (Promega), 200 μM dNTPs, 0.4 μmol/L (μM) of each
primer, 0.5U GoTaq polymerase (Promega) and 100ng DNA. Cycling conditions consisted of
95°C for 5 minutes; 30 cycles of 95°C for 30 seconds, 53°C for 30 seconds, and 72°C for 40
seconds; and a single cycle of 72°C for 7 minutes. PCR products were analysed by capillary
electrophoresis on the ABI 3100 Genetic Analyzer (Applied Biosystems). The GeneScan 500 Rox
size standard (Applied Biosystems) was used for size estimation of PCR products, and results
were analysed using GeneMapper software (version 3, Applied Biosystems). Microsatellite
alleles were called based on size, and organised into "bins" as specified by Greenberg et al.,
(2006) (Supplementary information). At least two samples from the Greenberg study cohort
were included with each experiment to ensure consistency of allele calls.

Supplementary table 1: Allele bins for SCA7 haplotype markers

Marker AC1
Allele Fragment size
(+-0.5, in base pairs)
1 167.32
2 171.14
3 172.91
4 175.02
5 176.97
6 178.91
7 180.81

Marker D3S1287
Allele Fragment size
(+-0.5, in base pairs)
1 241.03
5 253.04
2 254.83
3 256.8
4 258.77

The SNP rs3774729 was genotyped by direct sequencing. The PCR was carried out in a 25μl
reaction with 1x GoTaq Buffer (Promega), 200μM dNTPs (Bioline), 0.4μM of each primer, 0.5U
GoTaq Polymerase (Promega), and 100ng DNA. Cycling conditions were 95°C for 5 minutes; 30
cycles of 95°C for 30 seconds, 61°C for 30 seconds and 72°C for 40 seconds; single cycle of 72°C
for 7 minutes. PCR products were sequenced using a standard cycle sequencing reaction and
conditions. In a 10μl reaction: 1x BigDye Terminator Sequencing Buffer (Applied Biosystems), 1μl
BigDye Terminator v3.1 Cycle Sequencing RR-100 (Applied Biosystems), 0.4uM forward primer,
2μl PCR product. Cycling: 98°C for 5 minutes, followed by 25 cycles of 96°C for 10 seconds, 50°C
for 15 seconds, 60°C for 4 minutes. Sequencing products were precipitated with ethanol and
analysed on the ABI 3100 Genetic Analyzer. Sequence alignments were performed using the
BioEdit Sequence Alignment Editor (version 7.0.9.0).