Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease

The sequence of the human genome

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A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes

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Identification of the Cystic Fibrosis Gene: Cloning and Characterization of Complementary DNA

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A Strong Candidate for the Breast and Ovarian Cancer Susceptibility Gene BRCA1

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The Structure of Haplotype Blocks in the Human Genome

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The Future of Genetic Studies of Complex Human Diseases

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Identification of the Cystic Fibrosis Gene: Genetic Analysis

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A novel MHC class I-like gene is mutated in patients with hereditary haemochromatosis

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Identification of the breast cancer susceptibility gene BRCA2

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The Autism Genome Project

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Single-nucleotide polymorphisms detected in expressed sequence tags of melon (Cucumis meloL.)

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Bayesian Spatial Modeling of Haplotype Associations

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No association with hypertension of CLCNKB and TNFRSF1B polymorphisms at a hypertension locus on chromosome 1p36

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No major role of common SV2A variation for predisposition or levetiracetam response in epilepsy

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Structural and Functional Restraints on the Occurrence of Single Amino Acid Variations in Human Proteins

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Nutrigenetics and personalised nutrition: how far have we progressed and are we likely to get there?

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Familial combined hyperlipidemia: upstream transcription factor 1 and beyond

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Haplotype‐based association analysis in cohort studies of unrelated individuals

Lin, D. Y. (2004) · Genetic Epidemiology · doi:10.1002/gepi.10317 · Cited by 44

Where Do We Stand in the Quest for Neuropsychiatric Biomarkers and Endophenotypes and What Next?

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Dissecting Disease Inheritance Modes in a Three-Dimensional Protein Network Challenges the “Guilt-by-Association” Principle

Guo, Y., Wei, X., Das, J., Grimson, A., Lipkin, S. M., Clark, A. G., & Yu, H. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.05.022 · Cited by 44

Whole genome and exome sequencing of monozygotic twins discordant for Crohn’s disease

Petersen, B., Spehlmann, M. E., Raedler, A., Stade, B., Thomsen, I., Rabionet, R., Rosenstiel, P. C., Schreiber, S., & Franke, A. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-564 · Cited by 44

Review: Understanding Rare Genetic Diseases in Low Resource Regions Like Jammu and Kashmir – India

Angural, A., Spolia, A., Mahajan, A., Verma, V., Sharma, A., Kumar, P., Dhar, M. K., Pandita, K. K., Rai, E., & Sharma, S. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00415 · Cited by 44

Thrombomodulin gene polymorphisms or haplotypes as potential risk factors for venous thromboembolism: a population‐based case–control study

Heit, J. A., Petterson, T. M., Owen, W. G., BURKE, J. P., de Andrade, M., & Melton, L. J. (2005) · Journal of Thrombosis and Haemostasis · doi:10.1111/j.1538-7836.2005.01187.x · Cited by 44

Non-major-histocompatibility-complex genetics of ankylosing spondylitis

BROWNMBBSMDFRACP, M. (2006) · Best Practice & Research Clinical Rheumatology · doi:10.1016/j.berh.2006.03.005 · Cited by 44

Research Review: Crossing syndrome boundaries in the search for brain endophenotypes

Levy, Y., & Ebstein, R. P. (2008) · Journal of Child Psychology and Psychiatry · doi:10.1111/j.1469-7610.2008.01986.x · Cited by 44

Integrating human omics data to prioritize candidate genes

Chen, Y., Wu, X., & Jiang, R. (2013) · BMC Medical Genomics · doi:10.1186/1755-8794-6-57 · Cited by 42

Endocrinology Meets Metabolomics: Achievements, Pitfalls, and Challenges

Tokarz, J., Haid, M., Cecil, A., Prehn, C. P., Artati, A., Möller, G., & Adamski, J. (2017) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2017.07.001 · Cited by 44

DISNET: a framework for extracting phenotypic disease information from public sources

García, G. L., Rodríguez‐González, A., Santamaría, L. P., del Valle, E. P. G., Zanin, M., & Menasalvas, E. (2020) · PeerJ · doi:10.7717/peerj.8580 · Cited by 44

Unraveling A Complex Genetic Disease: Age-related Macular Degeneration

Chamberlain, M., Baird, P. N., Dirani, M., & Guymer, R. H. (2006) · Survey of Ophthalmology · doi:10.1016/j.survophthal.2006.08.003 · Cited by 42

Genetic and Immunologic Aspects of Sleep and Sleep Disorders

Parish, J. M. (2013) · CHEST Journal · doi:10.1378/chest.12-1219 · Cited by 43

Prioritization of candidate disease genes by topological similarity between disease and protein diffusion profiles

Zhu, J., Qin, Y., Liu, T., Wang, J., & Zheng, X. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-s5-s5 · Cited by 42

Next-Generation Sequencing to Diagnose Muscular Dystrophy, Rhabdomyolysis, and HyperCKemia

Wu, L., Brady, L., Shoffner, J. M., & Tarnopolsky, M. A. (2018) · Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques · doi:10.1017/cjn.2017.286 · Cited by 42

Deep Collaborative Filtering for Prediction of Disease Genes

Zeng, X., Lin, Y., He, Y., Lü, L., Min, X., & Rodríguez‐Patón, A. (2019) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2019.2907536 · Cited by 42

PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact

Li, F., Fan, C., Marquez‐Lago, T. T., Leier, A., Revote, J., Jia, C., Zhu, Y. L., Smith, A. I., Webb, G. I., Liu, Q., et al. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz050 · Cited by 42

Genomics, Genetics, and Plant Breeding

Cooper, M., Smith, O. S., Graham, G., Arthur, L., Feng, L., & Podlich, D. (2004) · Crop Science · doi:10.2135/cropsci2004.1907 · Cited by 42

The strange case of the ‘lumper’ lamin A/C gene and human premature ageing

Novelli, G., & D’Apice, M. R. (2003) · Trends in Molecular Medicine · doi:10.1016/s1471-4914(03)00162-x · Cited by 42

The sodium‐dependent glucose cotransporter SLC5A11 as an autoimmune modifier gene in SLE

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Rapid and Label-Free Single-Nucleotide Discrimination via an Integrative Nanoparticle–Nanopore Approach

Ang, Y. S., & Yung, L. L. (2012) · ACS Nano · doi:10.1021/nn302636z · Cited by 41

The rapid evolution of molecular genetic diagnostics in neuromuscular diseases

Volk, A. E., & Kubisch, C. (2017) · Current Opinion in Neurology · doi:10.1097/wco.0000000000000478 · Cited by 43

Matching Genotype and Phenotype: A Pragmatist Semiotic Analysis of Clinical Exome Sequencing

Timmermans, S. (2017) · American Journal of Sociology · doi:10.1086/692350 · Cited by 42

Identification of low penetrance alleles for lung cancer: The GEnetic Lung CAncer Predisposition Study (GELCAPS)

Eisen, T. G., Matakidou, A., & Houlston, R. S. (2008) · BMC Cancer · doi:10.1186/1471-2407-8-244 · Cited by 41

Various Pharmacogenetic Aspects of Antiepileptic Drug Therapy

Mann, M., & Pons, G. (2007) · CNS Drugs · doi:10.2165/00023210-200721020-00005 · Cited by 41

Molecular genetic pathways in Parkinson's disease: a review

Jain, S., Wood, N. W., & Healy, D. G. (2005) · Clinical Science · doi:10.1042/cs20050106 · Cited by 42

Whole genome association studies in complex diseases: where do we stand?

Need, A. C., & Goldstein, D. B. (2010) · Dialogues in Clinical Neuroscience · doi:10.31887/dcns.2010.12.1/aneed · Cited by 40

Identification of a PKP2 gene deletion in a family with arrhythmogenic right ventricular cardiomyopathy

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Rare Variants in Ischemic Stroke: An Exome Pilot Study

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Machine learning for bioinformatics and neuroimaging

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Single Nucleotide Polymorphisms Associated with Hepatocellular Carcinoma in Patients with Chronic Hepatitis B Virus Infection

Kim, Y. J., & Lee, H.-S. (2005) · Intervirology · doi:10.1159/000082089 · Cited by 40

ABCB4 sequence variations in young adults with cholesterol gallstone disease

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Prediction of Progression to Cirrhosis by a Glutathione S-Transferase P1 Polymorphism in Subjects With Hereditary Hemochromatosis

Stickel, F., Österreicher, C. H., Datz, C., Ferenci, P., Wölfel, M., Norgauer, W., Kraus, M. R., Wrba, F., Hellerbrand, C., & Schuppan, D. (2005) · Archives of Internal Medicine · doi:10.1001/archinte.165.16.1835 · Cited by 40

Single-molecule analysis for molecular haplotyping

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Genetic architecture of quantitative traits and complex diseases

Fu, W., O’Connor, T. D., & Akey, J. M. (2013) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2013.10.008 · Cited by 40

Host genetic studies in adult pulmonary tuberculosis

Meyer, C. G., & Thye, T. (2014) · Seminars in Immunology · doi:10.1016/j.smim.2014.09.005 · Cited by 39

A systematic characterization of genes underlying both complex and Mendelian diseases

Jin, W., Qin, P., Lou, H., Li, J., & Xu, S. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr599 · Cited by 40

Genetics of movement disorders in the next‐generation sequencing era

Olgiati, S., Quadri, M., & Bonifati, V. (2016) · Movement Disorders · doi:10.1002/mds.26521 · Cited by 43

Disease gene prioritization by integrating tissue-specific molecular networks using a robust multi-network model

Ni, J., Koyutürk, M., Tong, H., Haines, J. L., Xu, R., & Zhang, X. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1317-x · Cited by 39

A decade of next‐generation sequencing in genodermatoses: the impact on gene discovery and clinical diagnostics*

Chiu, F. P., Doolan, B. J., McGrath, J. A., & Onoufriadis, A. (2020) · British Journal of Dermatology · doi:10.1111/bjd.19384 · Cited by 40

The search for genenotype/phenotype associations and the phenome scan

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Human Pharmacogenomic Variations and Their Implications for Antifungal Efficacy

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Mitochondrial respiratory chain disorders in childhood: Insights into diagnosis and management in the new era of genomic medicine

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Gene discovery in familial cancer syndromes by exome sequencing: prospects for the elucidation of familial colorectal cancer type X

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Single Nucleotide Polymorphisms and Cancer Susceptibility

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A comparative computational approach toward pharmacological chaperones (NN-DNJ and ambroxol) on N370S and L444P mutations causing Gaucher's disease

Kumar, D. T., Iyer, S., Christy, J. P., Ramamoorthy, S., Tayubi, I. A., Doss, C. G. P., & Zayed, H. (2018) · Advances in protein chemistry and structural biology · doi:10.1016/bs.apcsb.2018.10.002 · Cited by 38

Applications of Next-Generation Sequencing in Systemic Autoimmune Diseases

Ma, Y., Shi, N., Li, M., Chen, F., & Niu, H. (2015) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.09.004 · Cited by 37

Bioinformatics Tools for Single Nucleotide Polymorphism Discovery and Analysis

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New mouse genetic models for human contraceptive development

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Failure to replicate an association of SNPs in the oxidized LDL receptor gene (OLR1) with CAD

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Genetic Susceptibility to Leprosy—From Classic Immune-Related Candidate Genes to Hypothesis-Free, Whole Genome Approaches

Cambri, G., & Mira, M. T. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.01674 · Cited by 42

A major locus for hereditary prostate cancer in Finland: localization by linkage disequilibrium of a haplotype in the HPCX region

Baffoe‐Bonnie, A. B., Smith, J. R., Stephan, D. A., Schleutker, J., Carpten, J. D., Kainu, T., Gillanders, E. M., Matikainen, M. P., Teslovich, T. M., Tammela, T. L. J., et al. (2005) · Human Genetics · doi:10.1007/s00439-005-1306-z · Cited by 37

Identification of Copy Number Variants Defining Genomic Differences among Major Human Groups

Armengol, L., Villatoro, S., González, J. R., Pantano, L., García‐Aragonés, M., Rabionet, R., Cáceres, M., & Estivill, X. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007230 · Cited by 38

Evolution of Premalignant DiseasePreprint

Curtius, K., Wright, N. A., & Graham, T. A. (2017) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a026542 · Cited by 38

Comparative yield of molecular diagnostic algorithms for autism spectrum disorder diagnosis in India: evidence supporting whole exome sequencing as first tier test

Sheth, F. J., Shah, J., Jain, D. K., Shah, S. N., Patel, H., Patel, K., Solanki, D., Iyer, A. S., Menghani, B., Mhatre, P., et al. (2023) · BMC Neurology · doi:10.1186/s12883-023-03341-0 · Cited by 38

NCAPG is differentially expressed during longissimus muscle development and is associated with growth traits in Chinese Qinchuan beef cattle

Liu, Y., Duan, X., Chen, S., He, H., & Liu, X. (2015) · Genetics and Molecular Biology · doi:10.1590/s1415-475738420140287 · Cited by 36

Disease classification: from phenotypic similarity to integrative genomics and beyond

Dozmorov, M. G. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bby049 · Cited by 36

Advances in genetics toward identifying pathogenic cell states of rheumatoid arthritis

Amariuta, T., Luo, Y., Knevel, R., Okada, Y., & Raychaudhuri, S. (2019) · Immunological Reviews · doi:10.1111/imr.12827 · Cited by 33

Association Study of 69 Genes in the Ret Pathway Identifies Low-penetrance Loci in Sporadic Medullary Thyroid Carcinoma

Ruiz‐Llorente, S., Montero‐Conde, C., Milne, R. L., Moya, C. M., Cebrián, A., Letón, R., Cascón, A., Mercadillo, F., Landa, I., Borrego, S., et al. (2007) · Cancer Research · doi:10.1158/0008-5472.can-07-1638 · Cited by 36

Affordable assays for genotyping single nucleotide polymorphisms in insects

Black, W. C., & VONTAS, J. G. (2007) · Insect Molecular Biology · doi:10.1111/j.1365-2583.2007.00736.x · Cited by 36

Dynamic Relationships between the Genome and Exposures to Environments as Causes of Common Human Diseases

Sing, C. F., Stengård, J., & Kardia, S. L. R. (2004) · KARGER eBooks · doi:10.1159/000081252 · Cited by 36

Finding genes in child psychology and psychiatry: When are we going to be there?

Plomin, R. J. (2005) · Journal of Child Psychology and Psychiatry · doi:10.1111/j.1469-7610.2005.01524.x · Cited by 36

HyMM: hybrid method for disease-gene prediction by integrating multiscale module structure

Xiang, J., Meng, X., Zhao, Y., Wu, F., & Li, M. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac072 · Cited by 34

Gene hunting in the genomic era: Approaches to diagnostic dilemmas in patients with primary immunodeficiencies

Platt, C. D., Geha, R. S., & Chou, J. S. (2013) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2013.08.021 · Cited by 37

Colorimetric Detection of DNA by Modulation of Thrombin Activity on Gold Nanoparticles

Jian, J., & Huang, C. (2011) · Chemistry - A European Journal · doi:10.1002/chem.201002825 · Cited by 35

Proband Whole-Exome Sequencing Identified Genes Responsible for Autosomal Recessive Non-Syndromic Hearing Loss in 33 Chinese Nuclear Families

Sang, S., Ling, J., Liu, X., Mei, L., Cai, X., Li, T., Li, W., Li, M., Wen, J., Liu, X., et al. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00639 · Cited by 35

The Linking of Sociology and Biology

Guo, G. (2006) · Social Forces · doi:10.1353/sof.2006.0126 · Cited by 36

Mapping Genes for Common Diseases: The Case for Genetic (LD) Maps

Collins, A. R., Lau, W., & Vega, F. M. D. L. (2004) · Human Heredity · doi:10.1159/000081451 · Cited by 35

Functional single nucleotide polymorphism-based association studies

Carlton, V. E. H., Ireland, J. S., Useche, F., & Faham, M. (2006) · Human Genomics · doi:10.1186/1479-7364-2-6-391 · Cited by 36

The Predicted Impact of Coding Single Nucleotide Polymorphisms Database

Rudd, M. F., Williams, R. D., Webb, E. L., Schmidt, S., Sellick, G. S., & Houlston, R. S. (2005) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-05-0469 · Cited by 35

Analysis of microsatellite markers and single nucleotide polymorphisms in candidate genes for susceptibility to bipolar affective disorder in the chromosome 12Q24.31 region

Shink, É., Harvey, M., Tremblay, M., Gagné, B., Belleau, P., Raymond, C., Labbé, M., Dubé, M., Lafrenière, R. G., & Barden, N. (2005) · American Journal of Medical Genetics Part B Neuropsychiatric Genetics · doi:10.1002/ajmg.b.30165 · Cited by 35

Using bioinformatics and genome analysis for new therapeutic interventions

Mount, D. W., & Pandey, R. (2005) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-05-0150 · Cited by 35

Genetics and Drug Use as a Complex Phenotype

Lessov, C. N., Swan, G. E., Ring, H. Z., Khroyan, T. V., & Lerman, C. E. (2004) · Substance Use & Misuse · doi:10.1081/ja-200033202 · Cited by 37

Genome wide association studies for diabetes: perspective on results and challenges

Torres, J., Cox, N. J., & Philipson, L. H. (2013) · Pediatric Diabetes · doi:10.1111/pedi.12015 · Cited by 33

Constructing an integrated gene similarity network for the identification of disease genes

Tian, Z., Guo, M., Wang, C., Xing, L., Wang, L., & Zhang, Y. (2017) · Journal of Biomedical Semantics · doi:10.1186/s13326-017-0141-1 · Cited by 34

Homozygosity mapping provides supporting evidence of pathogenicity in recessive Mendelian disease

Wakeling, M. N., Laver, T. W., Wright, C. F., Franco, E. D., Stals, K. L., Patch, A., Hattersley, A. T., Flanagan, S. E., & Ellard, S. (2018) · Genetics in Medicine · doi:10.1038/s41436-018-0281-4 · Cited by 34

Assessment of coding region variants in Kuwaiti population: implications for medical genetics and population genomics

John, S. E., Antony, D., Eaaswarkhanth, M., Hebbar, P., Channanath, A. M., Thomas, D., Devarajan, S., Tuomilehto, J., Al‐Mulla, F., Alsmadi, O. A., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-34815-8 · Cited by 33

PDGNet: Predicting Disease Genes Using a Deep Neural Network With Multi-View Features

Yang, K., Zheng, Y. F., Lu, K., Chang, K., Wang, N., Shu, Z., Yu, J. Q., Liu, B., Gao, Z., & Zhou, X. (2020) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2020.3002771 · Cited by 34

Comparative genomics analysis of human sequence variation in the UGT1A gene cluster

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