Supplementary Table 1. Association of rs2305089 in chordoma families with and without T duplication.
Sample status / Cases / Unaffected subjects / Regression Modela
Genotype / Genotype
rs2305089
CC(%) / CA(%) / AA(%) / CC(%) / CA(%) / AA(%) / OR / 95% CI / P
T dup / 0(0) / 10(62.5) / 6(37.5) / 8(32.0) / 12(48.0) / 5(20.0) / 2.72 / 0.83 / 8.96 / 0.1
No T dup / 0(0) / 3(42.9) / 4(57.1) / 3(11.1) / 9(33.3) / 15(55.6) / 2.29 / 0.33 / 15.91 / 0.4
All / 0(0) / 13(56.5) / 10(43.5) / 11(21.2) / 21(40.4) / 20(38.4) / 2.6 / 0.93 / 7.25 / 0.067
rs1056048
GG(%) / GA(%) / AA(%) / GG(%) / GA(%) / AA(%) / OR / 95% CI / P
T dup / 0(0) / 13(81.3) / 3(18.7) / 14(56.0) / 11(44.0) / 0(0) / N/A / N/A / N/A / N/A
No T dup / 3(37.5) / 4(50.0) / 1(12.5) / 11(39.3) / 15(53.6) / 2(7.1) / 1.19 / 0.31 / 4.49 / 0.8
All / 3(12.5) / 17(70.8) / 4(16.7) / 25(47.1) / 26(49.1) / 2(3.8) / 4.14 / 1.43 / 11.92 / 0.0086

aORs, 95%CIs, and P values were obtained using conditional logistic regression (log-additive) models comparing cases to all unaffected subjects (spouses and unaffected family members combined) conditioning on families to account for familial correlation.

Supplementary Table 2. Rare exonic T variants observed in sporadic cases
Prediction / Conservation
Location / dbSNP / Function / REF / VAR / SIFT / PolyPhen / MutationAssessor / MutationTaster / PhyloP / PhastCons / GERP
166571981 / rs368179445 / Missense / C / T / Tolerated / Probably Damaging / Medium / Disease causing / 3.64 / 0.748 / 4.05
166576021 / rs35694129 / Missense / G / A / Tolerated / Possibly Damaging / Low / Disease causing / 2.327 / 0.031 / 3.62
166581095 / rs3734509 / 5' UTR / C / T / N/A / N/A / N/A / Polymorphism / -0.195 / 0.008 / -0.00653

Supplementary Figure 1. Pedigrees for the two new chordoma families included in this study. (A). Family 5. Arrow: proband; Black upper quadrant: confirmed chordoma; Gray upper quadrant: suspected chordoma. There is only one confirmed chordoma case (proband’s father) in this family. The proband had a notochord remnant of the clivus (ecchordosis physaliphora) confirmed by histopathology at autopsy. A third relative (proband’s nephew) had a bilobed lesion associated with the clivus on magnetic resonance images, which is suspected to be a chordoma.(B). Family 9 with two confirmed chordoma cases.

(A).

(B).

Supplementary Figure 2. (A) Structure of the T-box region of X. laevis brachyury (green, PDB 1XBR) as a dimer bound to DNA (orange). The indicated amino acids represent the positions homologous to the human SNPs rs920961 (red), rs1056048 (blue), and rs2305089 (magenta). (B) The genomic structure and protein domains of the T gene and the encoded protein brachyury. Dotted lines indicate the approximate positions of the SNPs shown in (A). (C) Evolutionary conservation is assessed using a multiple alignment comparing sequences from H. sapiens (NP_003172.1), M. musculus (NP_033335.1), G. gallus (NP_990271.1), X. laevis (NP_001085165.1), D. rerio (NP_571237.1), S. kowalevskii (NP_001158367.1), T. castaneum (NP_001034532.1), D. melanogaster (NP_001261730.1), and C. intestinalis (NP_001027659.1).