Whole Genome Analysis in Consanguineous Families Reveals New Loci for Speech Sound Disorder (SSD)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification and Enrollment of Families
2.2. Collection and Evaluation of Speech Data
2.3. DNA Extraction and Whole-Genome SNP Genotyping
2.4. Linkage Analysis
2.5. Homozygosity Mapping
2.6. Haplotyping
3. Results
3.1. Speech Articulation Analysis
3.2. Linkage Analysis
3.3. Homozygosity Mapping and Haplotype Analysis
4. Discussion
5. Conclusions
6. Limitations
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Individual IDs | Addition Errors | Omission Errors | Substitution Errors | Total Errors | Correct Consonants | PCC |
---|---|---|---|---|---|---|
94001 | 0 | 0 | 10 | 10 | 74 | 88 |
94002 | 3 | 11 | 44 | 58 | 26 | 31 |
94003 | 1 | 0 | 2 | 3 | 81 | 96 |
94004 | 2 | 0 | 7 | 9 | 75 | 89 |
94006 | 0 | 0 | 14 | 14 | 70 | 83 |
94007 | 1 | 0 | 19 | 20 | 64 | 76 |
94008 | 1 | 2 | 33 | 36 | 48 | 57 |
94009 | 18 | 4 | 56 | 78 | 6 | 7 |
94010 | 0 | 0 | 0 | 0 | 84 | 100 |
94011 | 0 | 1 | 3 | 4 | 80 | 95 |
94012 | 0 | 0 | 4 | 4 | 80 | 95 |
94013 | 1 | 2 | 19 | 22 | 62 | 74 |
94014 | 0 | 2 | 2 | 4 | 80 | 95 |
94015 | 1 | 1 | 5 | 7 | 77 | 92 |
94016 | 2 | 0 | 22 | 24 | 60 | 71 |
94017 | 0 | 0 | 2 | 2 | 82 | 98 |
94018 | 0 | 0 | 1 | 1 | 83 | 99 |
94019 | 0 | 1 | 5 | 6 | 78 | 93 |
94020 | 0 | 1 | 6 | 7 | 77 | 92 |
94021 | 0 | 2 | 13 | 15 | 69 | 82 |
94022 | 1 | 2 | 3 | 6 | 78 | 93 |
94025 | 1 | 2 | 23 | 26 | 58 | 69 |
94026 | 2 | 3 | 25 | 30 | 54 | 64 |
94027 | 0 | 0 | 0 | 0 | 84 | 100 |
94028 | 0 | 2 | 9 | 11 | 73 | 87 |
94029 | 0 | 2 | 16 | 18 | 66 | 79 |
94030 | 0 | 0 | 1 | 1 | 83 | 99 |
94031 | 3 | 9 | 18 | 30 | 54 | 64 |
94032 | 0 | 2 | 8 | 10 | 74 | 88 |
94033 | 0 | 0 | 28 | 28 | 56 | 67 |
94034 | 1 | 3 | 15 | 19 | 65 | 77 |
94035 | 0 | 3 | 2 | 5 | 79 | 94 |
94036 | 0 | 0 | 4 | 4 | 80 | 95 |
94037 | 1 | 4 | 4 | 9 | 75 | 89 |
94038 | 1 | 12 | 41 | 54 | 30 | 36 |
94039 | 1 | 10 | 37 | 48 | 36 | 43 |
94046 | 3 | 3 | 32 | 38 | 46 | 55 |
94047 | 0 | 1 | 2 | 3 | 81 | 96 |
94058 | 1 | 1 | 7 | 9 | 75 | 89 |
94062 | 1 | 1 | 10 | 12 | 72 | 86 |
94063 | 5 | 0 | 25 | 30 | 54 | 64 |
Individual IDs | Addition Errors | Omission Errors | Substitution Errors | Total Errors | Correct Consonants | PCC |
---|---|---|---|---|---|---|
95001 | 3 | 3 | 25 | 31 | 53 | 63 |
95002 | 0 | 1 | 12 | 13 | 71 | 85 |
95003 | 0 | 1 | 9 | 10 | 74 | 88 |
95004 | 4 | 4 | 40 | 48 | 36 | 43 |
95005 | 0 | 1 | 7 | 8 | 76 | 90 |
95006 | 0 | 0 | 1 | 1 | 83 | 99 |
95007 | 0 | 0 | 1 | 1 | 83 | 99 |
95008 | 0 | 1 | 16 | 17 | 67 | 80 |
95009 | 0 | 0 | 6 | 6 | 78 | 93 |
95010 | 0 | 0 | 3 | 3 | 81 | 96 |
95011 | 0 | 1 | 5 | 6 | 78 | 93 |
95012 | 1 | 1 | 8 | 10 | 74 | 88 |
95013 | 4 | 5 | 18 | 27 | 57 | 68 |
95014 | 1 | 0 | 5 | 6 | 78 | 93 |
95015 | 0 | 0 | 0 | 0 | 84 | 100 |
Individual IDs | Addition Errors | Omission Errors | Substitution Errors | Total Errors | Correct Consonants | PCC |
---|---|---|---|---|---|---|
97001 | 0 | 2 | 21 | 23 | 61 | 73 |
97002 | 0 | 0 | 1 | 1 | 83 | 99 |
97003 | 0 | 1 | 7 | 8 | 76 | 90 |
97004 | 0 | 0 | 1 | 1 | 83 | 99 |
97005 | 0 | 0 | 14 | 14 | 70 | 83 |
97006 | 0 | 2 | 3 | 5 | 79 | 94 |
97007 | 3 | 0 | 6 | 9 | 75 | 89 |
97008 | 1 | 0 | 6 | 7 | 77 | 92 |
97009 | 0 | 0 | 12 | 12 | 72 | 86 |
97010 | 0 | 0 | 0 | 0 | 84 | 100 |
97011 | 0 | 0 | 0 | 0 | 84 | 100 |
97012 | 0 | 0 | 8 | 8 | 76 | 90 |
97013 | 0 | 1 | 9 | 10 | 74 | 88 |
97014 | 0 | 0 | 1 | 1 | 83 | 99 |
97015 | 0 | 1 | 14 | 15 | 69 | 82 |
97016 | 5 | 5 | 20 | 30 | 54 | 64 |
97017 | 0 | 1 | 11 | 12 | 72 | 86 |
97018 | 0 | 0 | 4 | 4 | 80 | 95 |
Chromosome | SNP ID | hg 19 Position (Mb) | Single-Point LOD Score |
---|---|---|---|
5 | rs1045706 | 108.714 | −2.157 |
5 | rs6879772 | 109.613 | 0.471 |
5 | rs381661 | 110.085 | 0.471 |
5 | rs456236 | 110.087 | 3.131 |
5 | rs6893213 | 110.198 | 0.471 |
5 | rs1837253 | 110.401 | 2.689 |
5 | rs10455025 | 110.404 | 3.131 |
5 | rs2162893 | 110.558 | 0.471 |
5 | rs115192 | 110.919 | 2.689 |
5 | rs27342 | 111.465 | 2.689 |
5 | rs1850407 | 112.721 | 3.131 |
5 | rs26959 | 112.736 | 3.131 |
5 | rs1496390 | 113.725 | 2.689 |
5 | rs28019 | 115.733 | 3.131 |
5 | rs1021516 | 116.544 | 0.471 |
5 | rs6891356 | 116.549 | 0.471 |
5 | rs13187808 | 117.223 | 3.131 |
5 | rs10079352 | 117.494 | 3.131 |
5 | rs13157174 | 117.912 | −1.912 |
Linkage Loci (hg 19) | Single-Point LOD Score | Mode of Inheritance | Affection Status | Family/ Branch | Homozygosity |
---|---|---|---|---|---|
16q12.1-q12.2 | 2.13 | Recessive | Phenotype | PKSLI-94 (Branch 1) | No |
6p22.1-p22.1 | 2.13 | Recessive | Phenotype | PKSLI-95 | No |
14q12-q21.1 | 2.80 | Recessive | Phenotype | PKSLI-95 | No |
5q21.3-5q23.1 | 3.13 | Recessive | Phenotype | PKSLI-97 | Yes |
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Yasmin, T.; Sadia, A.; Nadeem, L.; Basra, M.A.R.; Rice, M.L.; Raza, M.H. Whole Genome Analysis in Consanguineous Families Reveals New Loci for Speech Sound Disorder (SSD). Genes 2024, 15, 1069. https://doi.org/10.3390/genes15081069
Yasmin T, Sadia A, Nadeem L, Basra MAR, Rice ML, Raza MH. Whole Genome Analysis in Consanguineous Families Reveals New Loci for Speech Sound Disorder (SSD). Genes. 2024; 15(8):1069. https://doi.org/10.3390/genes15081069
Chicago/Turabian StyleYasmin, Tahira, Aatika Sadia, Laraib Nadeem, Muhammad Asim Raza Basra, Mabel L. Rice, and Muhammad Hashim Raza. 2024. "Whole Genome Analysis in Consanguineous Families Reveals New Loci for Speech Sound Disorder (SSD)" Genes 15, no. 8: 1069. https://doi.org/10.3390/genes15081069