Abstract
Mendelian mutations are the most medically actionable variants in the human genome and have always played a central role in its functional annotation. Despite the relative ease with which Mendelian mutations are identified compared to other classes of variants, the pace of their discovery has until recently been slow. However, recent technological advances in genomic sequencing have made the prospect of identifying all genes that can harbor Mendelian mutations an achievable near-term goal. The many lessons learned from previous discoveries of Mendelian mutations should inform future studies as I will discuss in this review. Also discussed are some of the challenges that will gain more prominence as we approach the last phase of the effort to map all Mendelian genes.
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Alazami AM, Alzahrani F, Bohlega S, Alkuraya FS (2014) SET binding factor 1 (SBF1) mutation causes Charcot-Marie-Tooth disease type 4B3. Neurology 82:1665–1666
Alazami AM, Patel N, Shamseldin HE, Anazi S, Al-Dosari MS, Alzahrani F, Hijazi H, Alshammari M, Aldahmesh MA, Salih MA (2015) Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families. Cell reports 10:148–161
Albers CA, Paul DS, Schulze H, Freson K, Stephens JC, Smethurst PA, Jolley JD, Cvejic A, Kostadima M, Bertone P (2012) Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome. Nat Genet 44:435–439
Aldahmesh MA, Khan AO, Mohamed J, Alkuraya FS (2011a) Novel recessive BFSP2 and PITX3 mutations: insights into mutational mechanisms from consanguineous populations. Genet Med 13:978–981
Aldahmesh MA, Mohamed JY, Alkuraya HS, Verma IC, Puri RD, Alaiya AA, Rizzo WB, Alkuraya FS (2011b) Recessive mutations in ELOVL4 cause ichthyosis, intellectual disability, and spastic quadriplegia. Am J Hum Genet 89:745–750
Aldahmesh MA, Khan AO, Alkuraya H, Adly N, Anazi S, Al-Saleh AA, Mohamed JY, Hijazi H, Prabakaran S, Tacke M (2013) Mutations in LRPAP1 are associated with severe myopia in humans. Am J Hum Genet 93:313–320
Alkuraya FS (2012) Discovery of rare homozygous mutations from studies of consanguineous pedigrees. Curr Protoc Hum Genet: 6.12. 1–6.12. 13
Alkuraya FS (2013) The application of next-generation sequencing in the autozygosity mapping of human recessive diseases. Hum Genet 132:1197–1211
Alkuraya FS (2015) Human knockout research: new horizons and opportunities. Trends Genet 31:108–115
Alsalem AB, Halees AS, Anazi S, Alshamekh S, Alkuraya FS (2013) Autozygome sequencing expands the horizon of human knockout research and provides novel insights into human phenotypic variation. PLoS Genet 9:e1004030
Al-Salem A, Alshammari MJ, Hassan H, Alazami AM, Alkuraya FS (2013) Weaver syndrome and defective cortical development: a rare association. Am J Med Genet Part A 161:225–227
Anazi S, Al-Sabban E, Alkuraya F (2014) Gonadal mosaicism as a rare cause of autosomal recessive inheritance. Clin Genet 85:278–281
Antonarakis SE, Beckmann JS (2006) Mendelian disorders deserve more attention. Nat Rev Genet 7:277–282
Antonarakis SE, Chakravarti A, Cohen JC, Hardy J (2010) Mendelian disorders and multifactorial traits: the big divide or one for all? Nat Rev Genet 11:380–384
Bohlega S, Alazami A, Cupler E, Al-Hindi H, Ibrahim E, Alkuraya F (2011) A novel syndromic form of sensory-motor polyneuropathy is linked to chromosome 22q13. 31–q13. 33. Clin Genet 79:193–195
Brinkman RR, Dubé M-P, Rouleau GA, Orr AC, Samuels ME (2006) Human monogenic disorders—a source of novel drug targets. Nat Rev Genet 7:249–260
Bühling F, Kouadio M, Chwieralski CE, Kern U, Hohlfeld JM, Klemm N, Friedrichs N, Roth W, Deussing JM, Peters C (2011) Gene targeting of the cysteine peptidase cathepsin H impairs lung surfactant in mice. PLoS One 6(10):e26247
Campbell IM, Gambin T, Jhangiani SN, Grove ML, Veeraraghavan N, Muzny DM, Shaw CA, Gibbs RA, Boerwinkle E, Yu F (2015) Multiallelic positions in the human genome: challenges for genetic analyses. Hum Mutat 37(3):231–234
Chong JX, Yu J-H, Lorentzen P, Park KM, Jamal SM, Tabor HK, Rauch A, Saenz MS, Boltshauser E, Patterson KE, Nickerson DA, Bamshad MJ (2015) Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features. Genet Med. doi:10.1038/gim.2015.161
Cirulli ET, Goldstein DB (2010) Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet 11:415–425
Elsea SH, Lucas RE (2002) The mousetrap: what we can learn when the mouse model does not mimic the human disease. ILAR J 43:66–79
Gai X, Ghezzi D, Johnson MA, Biagosch CA, Shamseldin HE, Haack TB, Reyes A, Tsukikawa M, Sheldon CA, Srinivasan S (2013) Mutations in FBXL4, encoding a mitochondrial protein, cause early-onset mitochondrial encephalomyopathy. Am J Hum Genet 93:482–495
Gilissen C, Hehir-Kwa JY, Thung DT, van de Vorst M, van Bon BW, Willemsen MH, Kwint M, Janssen IM, Hoischen A, Schenck A (2014) Genome sequencing identifies major causes of severe intellectual disability. Nature 511(7509):344–347
Group SM (2015) Comprehensive gene panels provide advantages over clinical exome sequencing for Mendelian diseases. Genome Biol 16:134
Hafner C, van Oers JM, Vogt T, Landthaler M, Stoehr R, Blaszyk H, Hofstaedter F, Zwarthoff EC, Hartmann A (2006) Mosaicism of activatingFGFR3 mutations in human skin causes epidermal nevi. J Clin Investig 116:2201
Huisman SA, Redeker EJ, Maas SM, Mannens MM, Hennekam RC (2013) High rate of mosaicism in individuals with Cornelia de Lange syndrome. J Med Genet 50:339–344
Indjeian VB, Kingman GA, Jones FC, Guenther CA, Grimwood J, Schmutz J, Myers RM, Kingsley DM (2016) Evolving new skeletal traits by cis-regulatory changes in bone morphogenetic proteins. Cell 164(1–2):45–56
Jamuar SS, Lam A-TN, Kircher M, D’Gama AM, Wang J, Barry BJ, Zhang X, Hill RS, Partlow JN, Rozzo A (2014) Somatic mutations in cerebral cortical malformations. N Engl J Med 371:733–743
Jordan DM, Frangakis SG, Golzio C, Cassa CA, Kurtzberg J, Davis EE, Sunyaev SR, Katsanis N (2015) Identification of cis-suppression of human disease mutations by comparative genomics. Nature 524:225–229
Kim J-I, Ju YS, Park H, Kim S, Lee S, Yi J-H, Mudge J, Miller NA, Hong D, Bell CJ (2009) A highly annotated whole-genome sequence of a Korean individual. Nature 460:1011–1015
Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, Gudjonsson SA, Sigurdsson A, Jonasdottir A, Jonasdottir A (2012) Rate of de novo mutations and the importance of father/’s age to disease risk. Nature 488:471–475
Lambertson KF, Damiani SA, Might M, Shelton R, Terry SF (2015) Participant-driven matchmaking in the genomic era. Hum Mutat 36:965–973
Lupski JR (2013) Genome mosaicism-one human, multiple genomes. Science 341:358–359
Lupski JR, Reid JG, Gonzaga-Jauregui C, Rio Deiros D, Chen DC, Nazareth L, Bainbridge M, Dinh H, Jing C, Wheeler DA (2010) Whole-genome sequencing in a patient with Charcot–Marie–Tooth neuropathy. N Engl J Med 362:1181–1191
MacArthur D, Manolio T, Dimmock D, Rehm H, Shendure J, Abecasis G, Adams D, Altman R, Antonarakis S, Ashley E (2014) Guidelines for investigating causality of sequence variants in human disease. Nature 508:469–476
Marotta CA, Wilson JT, Forget BG, Weissman SM (1977) Human beta-globin messenger RNA. III. Nucleotide sequences derived from complementary DNA. J Biol Chem 252:5040–5053
Might M, Wilsey M (2014) The shifting model in clinical diagnostics: how next-generation sequencing and families are altering the way rare diseases are discovered, studied, and treated. Genet Med 16(10):736–737
Nakhro K, Park J-M, Hong YB, Park JH, Nam SH, Yoon BR, Yoo JH, Koo H, Jung S-C, Kim H-L (2013) SET binding factor 1 (SBF1) mutation causes Charcot-Marie-Tooth disease type 4B3. Neurology 81:165–173
Pauling L, Itano HA, Singer SJ, Wells IC (1949) Sickle cell anemia, a molecular disease. Science 110:543–548
Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C (2015) The matchmaker exchange: a platform for rare disease gene discovery. Hum Mutat 36:915–921
Ronchi D, Di Fonzo A, Lin W, Bordoni A, Liu C, Fassone E, Pagliarani S, Rizzuti M, Zheng L, Filosto M (2013) Mutations in DNA2 link progressive myopathy to mitochondrial DNA instability. Am J Hum Genet 92:293–300
Sewairi W, Assiri A, Patel N, Alhashem A, Alkuraya FS (2016) Distal acroosteolysis, poikiloderma and joint stiffness: a novel laminopathy&quest. Eur J Hum Genet
Shaheen R, Alazami AM, Alshammari MJ, Faqeih E, Alhashmi N, Mousa N, Alsinani A, Ansari S, Alzahrani F, Al-Owain M (2012) Study of autosomal recessive osteogenesis imperfecta in Arabia reveals a novel locus defined by TMEM38B mutation. J Med Genet 49:630–635
Shaheen R, Aglan M, Keppler-Noreuil K, Faqeih E, Ansari S, Horton K, Ashour A, Zaki MS, Al-Zahrani F, Cueto-González AM (2013a) Mutations in EOGT confirm the genetic heterogeneity of autosomal-recessive Adams-Oliver syndrome. Am J Hum Genet 92:598–604
Shaheen R, Ansari S, Alshammari MJ, Alkhalidi H, Alrukban H, Eyaid W, Alkuraya FS (2013b) A novel syndrome of hypohidrosis and intellectual disability is linked to COG6 deficiency. J Med Genet 50:431–436
Shaheen R, Faqeih E, Ansari S, Abdel-Salam G, Al-Hassnan ZN, Al-Shidi T, Alomar R, Sogaty S, Alkuraya FS (2014a) Genomic analysis of primordial dwarfism reveals novel disease genes. Genome Res 24:291–299
Shaheen R, Rahbeeni Z, Alhashem A, Faqeih E, Zhao Q, Xiong Y, Almoisheer A, Al-Qattan SM, Almadani HA, Al-Onazi N (2014b) Neu-Laxova syndrome, an inborn error of serine metabolism, is caused by mutations in PHGDH. Am J Hum Genet 94:898–904
Shaheen R, Patel N, Shamseldin H, Alzahrani F, Al-Yamany R, Al A, Ewida N, Anazi S, Alnemer M, Elsheikh M, Alfaleh K, Alshammari M, Alhashem A, Alangari AA, Salih MA, Kircher M, Daza RM, Ibrahim N, Wakil SM, Alaqeel A, Altowaijri I, Shendure J, Al-Habib A, Faqieh E, Alkuraya FS (2015) Accelerating matchmaking of novel dysmorphology syndromes through clinical and genomic characterization of a large cohort. Genet Med. doi:10.1038/gim.2015.147
Shamseldin HE, Alshammari M, Al-Sheddi T, Salih MA, Alkhalidi H, Kentab A, Repetto GM, Hashem M, Alkuraya FS (2012a) Genomic analysis of mitochondrial diseases in a consanguineous population reveals novel candidate disease genes. J Med Genet 49:234–241
Shamseldin HE, Swaid A, Alkuraya FS (2012b) Lifting the lid on unborn lethal Mendelian phenotypes through exome sequencing. Genet Med 15:307–309
Shamseldin H, Alazami AM, Manning M, Hashem A, Caluseiu O, Tabarki B, Esplin E, Schelley S, Innes AM, Parboosingh JS (2015a) RTTN mutations cause primary microcephaly and primordial Dwarfism in humans. Am J Hum Genet 97:862–868
Shamseldin HE, Tulbah M, Kurdi W, Nemer M, Alsahan N, Al Mardawi E, Khalifa O, Hashem A, Kurdi A, Babay Z (2015b) Identification of embryonic lethal genes in humans by autozygosity mapping and exome sequencing in consanguineous families. Genome Biol 16:116
Shamseldin HE, Faqeih E, Alasmari A, Zaki MS, Gleeson JG, Alkuraya FS (2015b) Mutations in UNC80, Encoding Part of the UNC79-UNC80-NALCN Channel Complex, Cause Autosomal-Recessive Severe Infantile Encephalopathy. Am J Hum Genet
Shamseldin HE, Bennett AH, Alfadhel M, Gupta V, Alkuraya FS (2016) GOLGA2, encoding a master regulator of golgi apparatus, is mutated in a patient with a neuromuscular disorder. Hum Genet 135:245–251
Sobreira N, Schiettecatte F, Valle D, Hamosh A (2015) GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. Hum Mutat 36:928–930
Veltman JA, Brunner HG (2012) De novo mutations in human genetic disease. Nat Rev Genet 13:565–575
Vissers LE, de Ligt J, Gilissen C, Janssen I, Steehouwer M, de Vries P, van Lier B, Arts P, Wieskamp N, del Rosario M (2010) A de novo paradigm for mental retardation. Nat Genet 42:1109–1112
Wieczorek D, Newman WG, Wieland T, Berulava T, Kaffe M, Falkenstein D, Beetz C, Graf E, Schwarzmayr T, Douzgou S (2014) Compound heterozygosity of low-frequency promoter deletions and rare loss-of-function mutations in TXNL4A causes Burn-McKeown syndrome. Am J Hum Genet 95:698–707
Yavarna T, Al-Dewik N, Al-Mureikhi M, Ali R, Al-Mesaifri F, Mahmoud L, Shahbeck N, Lakhani S, AlMulla M, Nawaz Z (2015) High diagnostic yield of clinical exome sequencing in Middle Eastern patients with Mendelian disorders. Hum Genet 134:967–980
Acknowledgments
I thank Ranad Shaheen and Hanan E Shamseldin for their critical review of this manuscript. FSA was supported by a grant from King Salman Center for Disability Research and a grant from King Abdulaziz City for Science and Technology (13-BIO1113-20).
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Alkuraya, F.S. Discovery of mutations for Mendelian disorders. Hum Genet 135, 615–623 (2016). https://doi.org/10.1007/s00439-016-1664-8
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DOI: https://doi.org/10.1007/s00439-016-1664-8