Additional file 1 of A neurodegenerative disease landscape of rare mutations in Colombia due to founder effects
Creators: name: Acosta-Uribe, Juliana
name: Aguillón, David
name: Cochran, J. Nicholas
name: Giraldo, Margarita
name: Madrigal, Lucía
name: Killingsworth, Bradley W.
name: Singhal, Rijul
name: Labib, Sarah
name: Alzate, Diana
name: Velilla, Lina
name: Moreno, Sonia
name: García, Gloria P.
name: Saldarriaga, Amanda
name: Piedrahita, Francisco
name: Hincapié, Liliana
name: López, Hugo E.
name: Perumal, Nithesh
name: Morelo, Leonilde
name: Vallejo, Dionis
name: Solano, Juan Marcos
name: Reiman, Eric M.
name: Surace, Ezequiel I.
name: Itzcovich, Tatiana
name: Allegri, Ricardo
name: Sánchez-Valle, Raquel
name: Villegas-Lanau, Andrés
name: White, Charles L.
name: Matallana, Diana
name: Myers, Richard M.
name: Browning, Sharon R.
name: Lopera, Francisco
name: Kosik, Kenneth S.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Demographic information of the TANGL cohort and the Colombian population. Figure S2. Pipeline for whole genome sequence data quality control (QC). Figure S3. Principal Component Analysis of whole genomes from 1000 Genomes project and the TANGL cohort. Figure S4. Cross validation error for unsupervised ADMIXTURE clustering analysis of the TANGL cohort probands. Figure S5. Cross Validation Error for unsupervised ADMIXTURE clustering of the multi-ancestral dataset (TANGL genomes with the European and African populations from the 1000GP and Native American genomes from Mao et al. Figure S6. Global ancestry proportions of the TANGL cohort calculated by ADMIXTURE and sum of RFMix local ancestry estimation. Figure S7. Correlation of global ancestry proportions calculated for each individual by two different software, RFMix sum of local ancestries vs ADMIXTURE. Figure S8. Principal component analyses of the African and European cohorts of the 1000GP, along with 43 Native American genomes and the TANGL cohort. Figure S9. Principal component analyses of the African and European cohorts of the 1000GP, along with 43 Native American genomes and the TANGL cohort colored according to their proportions of global ancestry. Figure S10. Correlation of the principal component 1 and 2 values and the global ancestry proportions. For the TANGL.AFR.EUR.NAT cohort. Figure S11. Principal component analyses of the TANGL cohort colored according to their proportions of global ancestry. Figure S12. Correlation of the principal component 1 and 2 values and the global ancestry proportions for the TANGL cohort using common variants (MAF &gt;10%). Figure S13. Correlation of the principal component 1 and 2 values and the global ancestry proportions for the TANGL cohort using common variants (MAF 5-10%). Figure S14. Pipeline of the curation of disease-causing variants in the TANGL cohort. Figure S15. Variant filtering of disease-causing variants in the TANGL cohort. Figure S16. Pedigrees of the families with pathogenic variants in PSEN1 (NM_000021). Figure S17. Pairwise identity by Descent (IBD) segments in the chromosomes that harbor the PSEN1 NM_000021 c.791C&gt;T (p. Pro264Leu) variant. Figure S18. Pairwise identity by Descent (IBD) segments in the chromosomes that harbor the PSEN1 NM_000021 c.428T&gt;C (p.Ile143Thr) variant. Figure S19. Pairwise identity by Descent (IBD) segments in the chromosomes that harbor the PSEN1 NM_000021 c.356C&gt;T (p.Thr119Ile) variant in Colombian individuals. Figure S20. Pairwise identity by Descent (IBD) segments carrying the PSEN1 NM_000021 c.356C&gt;T (p.Thr119Ile) variant in Colombian and Argentinian individuals. Figure S21. Pedigrees of the family with a pathogenic variant in PSEN2 (NM_000447). Figure S22. Depth and allele balance indicate a duplication including APP. Figure S23. Pedigrees of the families with pathogenic variants in MAPT (NM_005910). Figure S24. Pairwise identity by Descent (IBD) segments in the chromosomes that harbor the MAPT NM_005910 c.1189C&gt;T (p.Pro397Ser) variant. Figure S25. Pairwise identity by Descent (IBD) segments in the chromosomes that harbor the MAPT NM_005910 c.1189C&gt;T (p.Pro397Ser) variant from Colombian and Spanish families. Figure S26. Pedigrees of the families with pathogenic variants in TBK1 (NM_013254). Figure S27. Pairwise identity by Descent (IBD) segments in the chromosomes that harbor TBK1 NM_013254 c.1257_1258del (p.Val421Cfs) variant. Figure S28. Pedigree of the family with a pathogenic variant in TARDBP (NM_007375). Figure S29. Pedigree of the family with a pathogenic variant in GRN (NM_002087). Figure S30. Pairwise identity by Descent (IBD) segments in the chromosomes that harbor SQSTM1 NM_003900 c.1175C&gt;T (p.Pro392Leu) variant in the TANGL cohort. Figure S31. Alignment of the haplotypes that harbor SQSTM1 NM_003900 c.1175C&gt;T (p.Pro392Leu) variant in the TANGL and the 1000GP cohort. Figure S32. Pedigrees of the families with pathogenic variants in TUBA4A (NM_006000). Figure S33. Pairwise identity by Descent (IBD) segments in the chromosomes that harbor TUBA4A NM_006000 c.820C&gt;G (p.Pro274Ala) variant. Figure S34. Pedigrees of the families with pathogenic variants in UBQLN2 (NM_0013444) identified by the present study. Figure S35. Histological characterization of ceroid neuronal lipofuscinosis-4B (CNL4B) and Pedigree of the family. Figure S36. Histological characterization of hereditary diffuse leukoencephalopathy with spheroids (HDLS). Bottom row and Pedigree of the family. Figure S37. Alignment of the haplotypes that carry Strictly Damaging and Protein Truncating Variants in TREM2 present in more than 1 individual. Figure S38. Alignment of the haplotypes that carry Strictly Damaging and Protein Truncating Variants in ABCA7 present in more than 1 individual. Figure S39. Alignment of the haplotypes that carry Strictly Damaging and Protein Truncating Variants in SORL1 present in more than 1 individual. Figure S40. Alignment of the haplotypes that carry Strictly Damaging and Protein Truncating Variants in ADAM10 present in more than 1 individual. Figure S41. Maps of Colombia representing the place of origin of the families with disease causing variants.