Table 1.
Linkage Analysis in Region 12p[Note]
|
LOD for Family and Recombination Fraction (Θ) |
|||||||||||||||||
|
Position |
F1 |
F2 |
F1 and F2 |
||||||||||||||
| Marker | NCBI Build 34(kb) | deCODE Map(cM) | .00 | .01 | .05 | .10 | Max | .00 | .01 | .05 | .10 | Max | .00 | .01 | .05 | .10 | Max |
| GGAT2AC007406 | 197 | .00 | .33 | .88 | 1.06 | 1.06 | −4.14 | −1.04 | −.41 | −.18 | .01 | −4.14 | −.71 | .48 | .88 | .90 | |
| D12S352 | 531 | .00 | 3.40 | 3.49 | 3.45 | 3.14 | 3.49 | .84 | .82 | .72 | .59 | .84 | 4.24 | 4.31 | 4.16 | 3.73 | 4.31 |
| GAAA2AC021054 | 591 | 2.84 | 2.92 | 2.85 | 2.52 | 2.92 | .37 | .37 | .33 | .28 | .37 | 3.22 | 3.29 | 3.18 | 2.80 | 3.29 | |
| GAAA1AC021054 | 650 | 4.69 | 4.73 | 4.57 | 4.14 | 4.73 | .00 | .00 | .00 | .00 | .00 | 4.69 | 4.73 | 4.57 | 4.14 | 4.73 | |
| CA1AC021054 | 652 | 2.94 | 3.02 | 2.95 | 2.63 | 3.02 | .37 | .37 | .33 | .28 | .37 | 3.32 | 3.39 | 3.28 | 2.91 | 3.39 | |
| CA2AC021054 | 656 | 5.10 | 5.07 | 4.81 | 4.36 | 5.10 | .97 | .94 | .82 | .67 | .97 | 6.07 | 6.01 | 5.63 | 5.03 | 6.07 | |
| GAAA3AC021054 | 701 | 2.54 | 2.56 | 2.54 | 2.37 | 2.56 | −.64 | −.41 | −.07 | .05 | .09 | 1.91 | 2.15 | 2.46 | 2.42 | 2.46 | |
| D12S341 | 719 | 5.10 | 4.98 | 4.48 | 3.86 | 5.10 | .08 | .08 | .07 | .06 | .08 | 5.18 | 5.06 | 4.55 | 3.92 | 5.18 | |
| CA1AC004765 | 756 | 5.50 | 5.37 | 4.83 | 4.16 | 5.50 | .11 | .13 | .17 | .18 | .18 | 5.61 | 5.50 | 5.00 | 4.34 | 5.61 | |
| CA2AC004765 | 771 | .95 | .93 | .82 | .70 | .95 | .00 | .00 | .00 | .00 | .00 | .95 | .92 | .82 | .70 | .95 | |
| D12S94 | 781 | 7.26 | 7.12 | 6.54 | 5.80 | 7.26 | .00 | .00 | .00 | .00 | .00 | 7.26 | 7.12 | 6.54 | 5.80 | 7.26 | |
| D12S91 | 817 | 1.03 | 5.08 | 4.96 | 4.45 | 3.81 | 5.08 | .37 | .37 | .33 | .28 | .37 | 5.46 | 5.32 | 4.78 | 4.09 | 5.46 |
| CA1AC004803 | 876 | 4.26 | 4.14 | 3.69 | 3.12 | 4.26 | .97 | .94 | .82 | .67 | .97 | 5.22 | 5.08 | 4.50 | 3.79 | 5.22 | |
| D12S389 | 984 | 1.69 | 3.88 | 3.80 | 3.46 | 2.99 | 3.88 | .37 | .37 | .33 | .28 | .37 | 4.25 | 4.17 | 3.78 | 3.27 | 4.25 |
| A1AC004803 | 963 | .66 | .63 | .53 | .41 | .66 | .37 | .37 | .33 | .28 | .37 | 1.03 | .99 | .86 | .69 | 1.03 | |
| D12S1285 | 1404 | 6.54 | 6.41 | 5.88 | 5.20 | 6.54 | .97 | .94 | .82 | .67 | .97 | 7.51 | 7.35 | 6.70 | 5.86 | 7.51 | |
| D12S1608 | 1629 | 3.65 | 4.80 | 4.68 | 4.19 | 3.58 | 4.80 | .97 | .94 | .82 | .67 | .97 | 5.77 | 5.61 | 5.00 | 4.24 | 5.77 |
| CA1AC005182 | 1631 | 6.56 | 6.43 | 5.88 | 5.17 | 6.56 | .97 | .94 | .82 | .67 | .97 | 7.53 | 7.36 | 6.69 | 5.84 | 7.53 | |
| D12S1656 | 1677 | 4.12 | 3.12 | 3.02 | 2.66 | 2.21 | 3.12 | .97 | .94 | .82 | .67 | .97 | 4.08 | 3.96 | 3.47 | 2.88 | 4.08 |
| CA1AC005183 | 1691 | 2.14 | 2.07 | 1.82 | 1.51 | 2.14 | .97 | .94 | .82 | .67 | .97 | 3.10 | 3.01 | 2.64 | 2.18 | 3.10 | |
| CA3AC005343 | 1744 | 3.73 | 3.62 | 3.20 | 2.68 | 3.73 | .97 | .94 | .82 | .67 | .97 | 4.69 | 4.56 | 4.02 | 3.35 | 4.69 | |
| CA2AC005343 | 1781 | 5.98 | 5.97 | 5.72 | 5.21 | 5.98 | .97 | .94 | .82 | .67 | .97 | 6.95 | 6.91 | 6.53 | 5.87 | 6.95 | |
| CA1AC005343 | 1783 | 7.48 | 7.34 | 6.77 | 6.03 | 7.48 | .97 | .94 | .82 | .67 | .97 | 8.44 | 8.27 | 7.58 | 6.70 | 8.44 | |
| CA1AC090840 | 1876 | 6.82 | 6.68 | 6.12 | 5.41 | 6.82 | .97 | .94 | .82 | .67 | .97 | 7.78 | 7.62 | 6.94 | 6.07 | 7.78 | |
| D12S1642 | 1904 | 1.52 | 1.48 | 1.31 | 1.10 | 1.52 | .08 | .08 | .07 | .06 | .08 | 1.60 | 1.56 | 1.38 | 1.15 | 1.60 | |
| CA2AC005342 | 1973 | 6.53 | 6.40 | 5.86 | 5.17 | 6.53 | .97 | .94 | .82 | .67 | .97 | 7.50 | 7.33 | 6.67 | 5.83 | 7.50 | |
| CA1AC005342 | 2036 | 5.49 | 5.44 | 5.13 | 4.62 | 5.49 | .97 | .94 | .82 | .67 | .97 | 6.46 | 6.38 | 5.95 | 5.29 | 6.46 | |
| D12S100 | 2047 | 4.76 | 6.50 | 6.37 | 5.83 | 5.14 | 6.50 | .97 | .94 | .82 | .67 | .97 | 7.47 | 7.30 | 6.65 | 5.81 | 7.47 |
| D12S1689 | 2205 | 2.89 | 2.80 | 2.46 | 2.05 | 2.89 | .08 | .08 | .07 | .06 | .08 | 2.97 | 2.89 | 2.54 | 2.11 | 2.97 | |
| D12S1694 | 2256 | 4.76 | 7.46 | 7.32 | 6.73 | 5.98 | 7.46 | .97 | .94 | .82 | .67 | .97 | 8.43 | 8.25 | 7.55 | 6.65 | 8.43 |
| D12S1615 | 2640 | 5.64 | 3.67 | 3.87 | 4.03 | 3.81 | 4.03 | .00 | .00 | .00 | .00 | .00 | 3.67 | 3.87 | 4.03 | 3.81 | 4.03 |
| D12S1626 | 3166 | 7.07 | 2.88 | 2.97 | 2.93 | 2.62 | 2.97 | .97 | .94 | .82 | .67 | .97 | 3.84 | 3.91 | 3.74 | 3.29 | 3.91 |
| D12S1652 | 3583 | 9.04 | 3.51 | 3.58 | 3.46 | 3.07 | 3.58 | .97 | .94 | .82 | .67 | .97 | 4.48 | 4.52 | 4.28 | 3.73 | 4.52 |
| D12S1725 | 4316 | 13.14 | −1.14 | −.76 | −.11 | .16 | .23 | −4.35 | −1.16 | −.51 | −.27 | .00 | −5.49 | −1.92 | −.62 | −.11 | .14 |
| D12S1624 | 4581 | −1.56 | −1.22 | −.50 | −.11 | .13 | −4.50 | −1.06 | −.46 | −.26 | .00 | −6.06 | −2.28 | −.95 | −.37 | .05 | |
| D12S314 | 4839 | 13.96 | −1.24 | −.82 | −.08 | .25 | .37 | −4.50 | −1.06 | −.46 | −.26 | .00 | −5.74 | −1.88 | −.54 | −.01 | .25 |
| D12S93 | 5201 | 15.00 | −1.22 | −.91 | −.39 | −.18 | .00 | −.21 | −.20 | −.16 | −.10 | .00 | −1.43 | −1.11 | −.55 | −.28 | .00 |
| D12S99 | 5435 | 15.20 | −.83 | −.51 | .05 | .25 | .25 | −5.54 | −2.85 | −1.49 | −.93 | .00 | −6.37 | −3.36 | −1.43 | −.67 | .00 |
Note.— Samples from 15 family members from F1 and 7 family members from F2, including a total of seven living affected individuals from Newfoundland, were genome scanned. Genomic DNA was extracted from blood samples using a standard salt-extraction method. DNA was also obtained from tissue samples of one deceased individual in F1, previously diagnosed with HSAN type II. We carried out a 5-cM whole-genome screen using the LMS2 HD-5 microsatellite screening set (Applied Biosystems) and Prism 3100 and 3700 Genetic Analyzers running GeneMapper software (Applied Biosystems). For fine mapping, we analyzed an additional 16 Genethon markers and 1 CHLC marker (derived from NCBI, GDB, and Marshfield databases), and designed 18 novel markers containing short tandem repeats on the basis of publicly available genomic sequences. Genome-scan markers are indicated in boldface italics in the table. Primer sequences for all markers are indicated in table A1 (online only); map locations are described using the deCODE genetic maps (Kong et al. 2002) and physical locations are based on the July 2003 build 34 genome assembly. Mendelian inheritance of alleles was verified using the PedCheck program (O’Connell and Weeks 1998). We performed pairwise linkage analysis on the F1 and F2 pedigrees using MLINK from the FASTLINK v4.1p program (Cottingham et al. 1993; Schaffer et al. 1994) and allowing for known pedigree consanguinity loops. We calculated maximum pairwise cumulative LOD scores as the maximum LOD over tested Θ of the sum of Θ-specific LODs for the F1 and F2 pedigrees. We chose to not carry out multipoint linkage since pairwise results were sufficiently convincing and we wished to retain the consanguinity information of F1 for linkage. We set equal marker allele frequencies for the genomewide linkage scan. For the follow-up linkage analysis at 12p13, allele frequencies were estimated using 16 chromosomes from 8 unrelated individuals from the Newfoundland population, as well as 8 untransmitted chromosomes from F3 and F4 (F3-9, F3-10, F4-37, F4-38, F4-112, F4-122, F4-371). Frequencies were estimated using allele counting. Unobserved alleles were set to 0.02 frequency, and all frequencies were proportionally transformed to sum to 1. Two consanguineous loops of F1 were broken at individuals 15 and 708. We used an autosomal recessive model with a disease allele frequency of 0.007, penetrance of 0.975, and phenocopy rate of 0.000003, as calculated from the disease prevalence in the population. Linkage tests using equal allele frequencies were carried out in parallel for the fine-mapping data presented in the table. We believe that using the estimated allele frequencies from the Newfoundland population does provide more accurate LOD score estimates; however, LOD scores calculated using equal allele frequencies provided significant results as well, with a maximum LOD of 5.88 at D12S1285.