Chorea-Acanthocytosis Genotype in the Original Critchley Kentucky Neuroacanthocytosis Kindred

Supplementary Online Content

Velayos-Baeza A, Holinski-Feder E, Neitzel B, et al. Chorea-acanthocytosis genotype in the original Critchley Kentucky neuroacanthocytosis kindred. Arch Neurol. 2011;68(10):1330-1333.

eTable 1. Genotyping details. eTable 2. Allele distribution in the different haplotypes found. eTable 3. Haplotype distribution in members of the Kentucky and "proband 23" families. eFigure. Haplotype combinations in the Kentucky family.

This supplementary material has been provided by the authors to give readers additional information about their work.

Downloaded From: https://jamanetwork.com/ on 09/30/2021 eTable 1. Genotyping details. 7 Alleles found P 1 2 3 4 5 6 Marker P Altern. name Size/nt P Forward primer Reverse primer Dye P Position P cM P Mix P 1 2 3 4 5 6

D9S927 GATA28C02 118-134 TCTGTGAAACATATAAAGAAAATTGC TTTCCTCAGTACAAAACAATATGC PET -2969553 68.92312 A 123 127 133

D9S175 AFM224zh10 200-230 GTAATGTGCTAAATACCAGAGTTG CCCTTACCTAGAATGCCC VIC -1845045 70.64 C 204 206 208 210 222

D9S1122 GATA89A11 186-210 GCTTCTGAAAGCTTCTAGTTTACC AATAGTAATGCATTTGTGATAGG PET -103994 74.35 B 192 196 200

D9S1674 AFM144YE9 216-232 GGCCTACCCTGTAGACTGAC TTAGAAGTGAGCCAAACTCAAA 6FAM 128619 74.81128 B 212 216 220 224 226 230

c.7867 C / T TGTGAATTTTATGGACATGGG GCTAGCACAACATTGAAACTG - 180047 74.91326 - C T

c.9077-262 C / T - 204009 74.96078 - C T TCCGTAGGGTCAGGAATGAG TTAAGCAAAATAGATAAAAGCCC c.9077-133 rs10869920 A / G - 204138 74.96104 - A G

D9S1123 GATA89C08 342-366 AGCCCAAGCTTTTAACCACT GCTGCTTAGCTAAACATGGC 6FAM 632252 75.81 C 355 359 363 367

D9S153 AFM025yb2 143-155 TTATGGCAGCCCAAATGGACTA GCAGAATGTTGCCCAAAACTCA 6FAM 1788709 76.69892 C 141 143 145 147 149

D9S1780 AFMa121wh9 241-259 ACATTGTGTCTTATTCTGCATGA CGCTTTGTAAAGATAGCCTCA PET 2076329 76.92 C 244 246 248 250 252

D9S1843 AFMb321yf9 201-255 CCATAATTGTGTGAGCCAG CCACCATCGAGAAGTTAGTTT 6FAM 2746521 77.56 A 242 248 252

D9S303 GATA3D04 148-168 CAACAAAGCAAGATCCCTTC TAGGTACTTGGAAATTCTTGGC VIC 5098424 80.21524 B 150 154 158 162 166

D9S1785 AFMA137WF9 169-201 GTACTGGCAATATGCAAAG CCTGGGTCTGACAACATC VIC 5501234 80.67 A 192 194 198 200

1. Microsatellite markers in the region of chromosome 9 where the VPS13A gene is located were selected (specific data can be obtained from http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists). Positions c.7867 (exon 56) and c.9077-262 (intron 67), where changes were detected by the initial sequencing analysis, and SNP rs10869920 (c.9077-133, intron 67) were genotyped by direct sequencing. 2. Expected result for each marker; sizes in bp. 3. Forward primers (Reverse primer for D9S1785) were labelled with the listed dyes. 4. Position, in bp, relative to VPS13A gene, with A from ATG codon as position +1. 5. Genetic position, in cM, used for haplotype analysis with the Merlin software (data from the deCODE map, except values with 5 decimals which were calculated as linear values between two adjacent available data). 6. The labelled PCR products (from 25-µl reactions using 20ng of gDNA as a template) were combined in three multiplex mixes (A, B, C) at a final dilution of 1/50; 2µl of each mix were used for analysis. 7. The size (bp) or nucleotide for each analyzed marker is shown. Numbers 1 to 6 in each column are the allele numbers used for the microsatellite markers in haplotypes shown in eFigure 1 and eTable 2.

Downloaded From: https://jamanetwork.com/ on 09/30/2021 eTable 2. Allele distribution in the different haplotypes found. Haplotype # Marker Allele A B C D 1 2 3 4 5 6 7 8 9 10 11 haplot. 123 1 1 1 3 D9S927 127 2 2 2 2 2 2 2 2 2 2 10 133 3 3 2 204 1 1 1 1 1 1 1 7 206 2 1 D9S175 208 3 1 210 4 4 4 3 222 5 5 5 3 192 1 1 2 D9S1122 196 2 2 2 2 2 2 2 7 200 3 3 3 3 3 3 6 212 1 1 216 2 2 2 2 2 5 220 3 3 2 D9S1674 224 4 4 4 3 226 5 5 2 230 6 6 2 C C C C C C C C C C C C C C 13 c.7867 T T T 2 C C C C C C C C C C C C C C 13 Ex68-262 T T T 2 A A A A A A A A 7 Ex68-133 G G G G G G G G G 8 355 1 1 2 359 2 2 2 2 2 5 D9S1123 363 3 3 3 3 3 3 6 367 4 4 2 141 1 1 1 3 143 2 2 2 3 D9S153 145 3 3 3 3 147 4 1 149 5 5 5 5 5 5 244 1 1 2 246 2 1 D9S1780 248 3 3 3 3 3 3 3 7 250 4 4 4 3 252 5 5 2 242 1 1 1 1 1 1 1 7 D9S1843 248 2 2 2 252 3 3 3 3 3 3 6 150 1 1 1 3 154 2 2 2 D9S303 158 3 3 3 3 4 162 4 4 4 4 4 5 166 5 1 192 1a 1b 1b 1a 2 194 2b 2a 2a 2b 2 2 2 2 2 7 D9S1785 198 3 3 2 200 4 4 4 4 4

The alleles present in each haplotype are indicated with the “allele number” as shown in eTable 1; two options exist for D9S1785 (a / b) in haplotypes A-D. Haplotypes 1-11, found in the Kentucky family members, can be explained without recombination events. Haplotypes A-D, in "proband 23" ‘s family, are shown assuming no recombination (no information on recombination is available in trio families). The number of haplotypes carrying a specific allele is shown in the last column. A red box shows the region that seems to be shared by haplotypes D and 1 carrying the c.7867C>T mutation.

Downloaded From: https://jamanetwork.com/ on 09/30/2021 eTable 3. Haplotype distribution in members of the Kentucky and "proband 23" families. Haplotype Generation Member A B C D 1 2 3 4 5 6 7 8 9 10 11 4 h h II 5 h h 7 h h 8 h h 10 h h 11 h h 12 h h 13 h h 14 h h 16 h h 17 h h 19 h h 20 h h 29 h h 30 h h 31 h h 1 d d I 2 D 4 D 5 D 6 d 7 d d 8 h h 9 D 10 D 12 h h 1 d d1 d2 0 2 d d2 d1 3 d 4 d I-1-P2 h h Partners I-6-P h h I-7-P d d I-9-P d d Mother h h Prob. 23 family Father h h Proband h h

Only family members directly analyzed and those for which their haplotypes could be deduced are shown. No evidence of recombination events was found (see eTable 2) Key: h: Haplotype in tested individual, in heterozygosis D: Haplotype deduced, in homozygosis d: Haplotype deduced, in heterozygosis (2nd haplotype for I-6, 0-3 and 0-4 is not known) d1/d2: 2nd haplotype (deduced) in 0-1 and 0-2, in heterozygosis (both options are possible)

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0-1 0-2 0-3 0-4 Haplotype # Marker 1 2 3 4 5 6 7 8 9 10 11 1 2 or 3 1 3 or 2 6 ? 7 ? D9S927 1 2 2 2 2 1 3 2 2 2 1 1 2 2 1 2 2 1 3 D9S175 4 1 1 5 1 2 4 5 5 1 4 4 1 1 4 1 1 2 4 D9S1122 2 3 3 3 2 2 2 1 3 2 3 2 3 3 2 3 3 2 2 D9S1674 2 2 1 4 6 3 4 2 4 6 2 2 2 1 2 1 2 3 4 c.7867 T C C C C C C C C C C T C C T C C C C c.9077-262 T C C C C C C C C C C T C C T C C C C c.9077-133 A A A G G G G A G G A A A A A A A G G D9S1123 2 3 3 2 2 1 2 3 3 3 3 2 3 3 2 3 3 1 2 D9S153 5 2 5 3 2 1 2 3 5 5 1 5 2 5 5 5 2 1 2 D9S1780 5 4 3 3 3 1 4 3 3 4 1 5 4 3 5 3 4 1 4 D9S1843 3 1 2 1 1 3 3 3 1 1 1 3 1 2 3 2 1 3 3 D9S303 4 1 4 1 5 3 3 3 2 3 4 4 1 4 4 4 1 3 3 D9S1785 2 2 3 4 3 2 4 4 2 4 2 2 2 3 2 3 2 2 4

I-1 I-1-P2 I-2 I-3 I-4 I-5 I-6-P I-6 I-7 I-7-P I-8 I-9 I-9-P I-10 I-12

1 3 10 11 1 1 1 1 1 1 6 7 1 ? 2 3 8 9 1 2 1 1 4 5 1 1 1 6 1 2 2 1 1 1 1 1 1 1 1 3 1 2 2 2 2 1 2 1 1 2 2 1 1 1 1 4 1 1 4 4 4 4 4 4 4 2 4 4 1 1 5 5 4 1 4 4 5 1 4 4 4 2 2 3 2 3 2 2 2 2 2 2 2 2 2 3 3 1 3 2 3 2 2 3 2 2 2 2 2 2 1 6 2 2 2 2 2 2 2 3 4 2 2 1 2 4 2 2 2 2 4 6 2 2 2 3 T C C C T T T T T T C C T C C C C T C T T C C T T T C

T C C C T T T T T T C C T C C C C T C T T C C T T T C A A G A A A A A A A G G A A A A G A A A A G G A A A G 2 3 3 3 2 2 2 2 2 2 1 2 2 3 3 3 3 2 3 2 2 2 2 2 2 2 1 5 5 5 1 5 5 5 5 5 5 1 2 5 2 5 3 5 5 2 5 5 3 2 5 5 5 1 5 3 4 1 5 5 5 5 5 5 1 4 5 4 3 3 3 5 4 5 5 3 3 5 5 5 1 3 2 1 1 3 3 3 3 3 3 3 3 3 1 2 3 1 3 1 3 3 1 1 3 3 3 3 4 4 3 4 4 4 4 4 4 4 3 3 4 1 4 3 2 4 1 4 4 1 5 4 4 4 3 2 3 4 2 2 2 2 2 2 2 2 4 2 2 3 4 2 2 2 2 2 4 3 2 2 2 2

II-4 II-5 II-7 II-8 II-10 II-11 II-12 II-13 II-14 II-16 II-17 II-19 II-20 II-29 II-30 II-31

1 10 3 10 1 7 1 6 2 8 2 8 2 9 2 8 3 8 3 8 2 9 2 8 3 9 1 4 1 5 1 4 1 2 2 2 1 3 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 1 2 1 2 4 1 1 1 4 4 4 2 1 5 1 5 1 5 1 5 1 5 1 5 1 5 1 5 1 5 4 5 4 1 4 5 2 2 3 2 2 2 2 2 3 1 3 1 3 3 3 1 3 1 3 1 3 3 3 1 3 3 2 3 2 2 2 3 2 6 1 6 2 4 2 3 2 2 2 2 2 4 2 2 1 2 1 2 2 4 2 2 1 4 2 4 2 6 2 4

T C C C T C T C C C C C C C C C C C C C C C C C C C T C T C T C T C C C T C T C C C C C C C C C C C C C C C C C C C T C T C T C A G A G A G A G A A A A A G A A A A A A A G A A A G A G A G A G 2 3 3 3 2 2 2 1 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 5 5 5 5 5 2 5 1 2 3 2 3 2 5 2 3 5 3 5 3 2 5 2 3 5 5 5 3 5 2 5 3 5 4 3 4 5 4 5 1 4 3 4 3 4 3 4 3 3 3 3 3 4 3 4 3 3 3 5 3 5 3 5 3 3 1 2 1 3 3 3 3 1 3 1 3 1 1 1 3 2 3 2 3 1 1 1 3 2 1 3 1 3 1 3 1 4 3 4 3 4 3 4 3 1 3 1 3 1 2 1 3 4 3 4 3 1 2 1 3 4 2 4 1 4 5 4 1 2 4 3 4 2 4 2 2 2 4 2 4 2 2 2 4 3 4 3 4 2 2 2 4 3 2 2 4 2 3 2 4

eFigure. Haplotype combinations in the Kentucky family. Family members not analyzed and for whom haplotypes could not be deduced have been removed from the family tree, except I-3. Clinical information and symbols as shown in Fig.1. All haplotypes are shown in the table (top left); haplotype number appears on top and the corresponding allele for each marker is shown in color. Haplotypes for each individual are shown below the family-member identifier; haplotype number appears in black when a sample was directly analyzed, and in red when they were deduced from data obtained for other family members. Both parents of the original proband (I-10) are carriers for haplotype 1 which includes the c.7867C>T mutation; two options are possible for the second haplotype (2 & 3 or 3 & 2). 4

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