51
|
Shaheen R, Al Hashem A, Alghamdi MH, Seidahmad MZ, Wakil SM, Dagriri K, Keavney B, Goodship J, Alyousif S, Al-Habshan FM, Alhussein K, Almoisheer A, Ibrahim N, Alkuraya FS. Positional mapping ofPRKD1,NRP1andPRDM1as novel candidate disease genes in truncus arteriosus. J Med Genet 2015; 52:322-9. [DOI: 10.1136/jmedgenet-2015-102992] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/30/2015] [Indexed: 11/03/2022]
|
52
|
Tadmouri GO, Sastry KS, Chouchane L. Arab gene geography: From population diversities to personalized medical genomics. Glob Cardiol Sci Pract 2014; 2014:394-408. [PMID: 25780794 PMCID: PMC4355514 DOI: 10.5339/gcsp.2014.54] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/11/2014] [Indexed: 12/20/2022] Open
Abstract
Genetic disorders are not equally distributed over the geography of the Arab region. While a number of disorders have a wide geographical presence encompassing 10 or more Arab countries, almost half of these disorders occur in a single Arab country or population. Nearly, one-third of the genetic disorders in Arabs result from congenital malformations and chromosomal abnormalities, which are also responsible for a significant proportion of neonatal and perinatal deaths in Arab populations. Strikingly, about two-thirds of these diseases in Arab patients follow an autosomal recessive mode of inheritance. High fertility rates together with increased consanguineous marriages, generally noticed in Arab populations, tend to increase the rates of genetic and congenital abnormalities. Many of the nearly 500 genes studied in Arab people revealed striking spectra of heterogeneity with many novel and rare mutations causing large arrays of clinical outcomes. In this review we provided an overview of Arab gene geography, and various genetic abnormalities in Arab populations, including disorders of blood, metabolic, circulatory and neoplasm, and also discussed their associated molecules or genes responsible for the cause of these disorders. Although studying Arab-specific genetic disorders resulted in a high value knowledge base, approximately 35% of genetic diseases in Arabs do not have a defined molecular etiology. This is a clear indication that comprehensive research is required in this area to understand the molecular pathologies causing diseases in Arab populations.
Collapse
Affiliation(s)
| | - Konduru S Sastry
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar
| | - Lotfi Chouchane
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar
| |
Collapse
|
53
|
Human knockout research: new horizons and opportunities. Trends Genet 2014; 31:108-15. [PMID: 25497971 DOI: 10.1016/j.tig.2014.11.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/15/2014] [Accepted: 11/17/2014] [Indexed: 12/12/2022]
Abstract
Although numerous approaches have been pursued to understand the function of human genes, Mendelian genetics has by far provided the most compelling and medically actionable dataset. Biallelic loss-of-function (LOF) mutations are observed in the majority of autosomal recessive Mendelian disorders, representing natural human knockouts and offering a unique opportunity to study the physiological and developmental context of these genes. The restriction of such context to 'disease' states is artificial, however, and the recent ability to survey entire human genomes for biallelic LOF mutations has revealed a surprising landscape of knockout events in 'healthy' individuals, sparking interest in their role in phenotypic diversity beyond disease causation. As I discuss in this review, the potentially wide implications of human knockout research warrant increased investment and multidisciplinary collaborations to overcome existing challenges and reap its benefits.
Collapse
|
54
|
Khan AO, Aldahmesh MA, Alsharif H, Alkuraya FS. Recessive Mutations inLEPREL1Underlie a Recognizable Lens Subluxation Phenotype. Ophthalmic Genet 2014; 36:58-63. [DOI: 10.3109/13816810.2014.985847] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
55
|
Jalkh N, Sahbatou M, Chouery E, Megarbane A, Leutenegger AL, Serre JL. Genome-wide inbreeding estimation within Lebanese communities using SNP arrays. Eur J Hum Genet 2014; 23:1364-9. [PMID: 25424710 DOI: 10.1038/ejhg.2014.246] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 08/29/2014] [Accepted: 09/19/2014] [Indexed: 12/14/2022] Open
Abstract
Consanguineous marriages have been widely practiced in several global communities with varying rates depending on religion, culture, and geography. In consanguineous marriages, parents pass to their children autozygous segments known as homozygous by descent segments. In this study, single-nucleotide polymorphisms were analyzed in 165 unrelated Lebanese people from Greek Orthodox, Maronite, Shiite and Sunni communities. Runs of homozygosity, total inbreeding levels, remote consanguinity, and population admixture and structure were estimated. The inbreeding coefficient value was estimated to be 1.61% in offspring of unrelated parents over three generations and 8.33% in offspring of first cousins. From these values, remote consanguinity values, resulting from genetic drift or recurrent consanguineous unions, were estimated in offspring of unrelated and first-cousin parents to be 0.61 and 1.2%, respectively. This remote consanguinity value suggests that for any unrelated marriages in Lebanon, the mates could be related as third cousins or as second cousins once removed. Under the assumption that 25% of marriages occur between first cousins, the mean inbreeding value of 2.3% may explain the increased incidence of recessive disease in offspring. Our analysis reveals a common ancestral population in the four Lebanese communities we studied.
Collapse
Affiliation(s)
- Nadine Jalkh
- Unité de Génétique Médicale et Laboratoire associé INSERM à l'Unité UMR_S910, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon.,EA 2493 « pathologie cellulaire & génétique, de la conception à la naissance », Université de Versailles-Saint Quentin en Yvelines, Yvelines, France
| | | | - Eliane Chouery
- Unité de Génétique Médicale et Laboratoire associé INSERM à l'Unité UMR_S910, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon
| | - André Megarbane
- Unité de Génétique Médicale et Laboratoire associé INSERM à l'Unité UMR_S910, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon
| | | | - Jean-Louis Serre
- EA 2493 « pathologie cellulaire & génétique, de la conception à la naissance », Université de Versailles-Saint Quentin en Yvelines, Yvelines, France
| |
Collapse
|
56
|
Alkuraya FS. Genetics and genomic medicine in Saudi Arabia. Mol Genet Genomic Med 2014; 2:369-78. [PMID: 25333061 PMCID: PMC4190871 DOI: 10.1002/mgg3.97] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 06/30/2014] [Indexed: 01/01/2023] Open
Affiliation(s)
- Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center Riyadh, Saudi Arabia ; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University Riyadh, Saudi Arabia
| |
Collapse
|
57
|
Patel N, Smith LL, Faqeih E, Mohamed J, Gupta VA, Alkuraya FS. ZBTB42 mutation defines a novel lethal congenital contracture syndrome (LCCS6). Hum Mol Genet 2014; 23:6584-93. [PMID: 25055871 DOI: 10.1093/hmg/ddu384] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Lethal congenital contracture syndrome (LCCS) is a lethal autosomal recessive form of arthrogryposis multiplex congenita (AMC). LCCS is genetically heterogeneous with mutations in five genes identified to date, all with a role in the innervation or contractile apparatus of skeletal muscles. In a consanguineous Saudi family with multiple stillbirths presenting with LCCS, we excluded linkage to all known LCCS loci and combined autozygome analysis and whole-exome sequencing to identify a novel homozygous variant in ZBTB42, which had been shown to be enriched in skeletal muscles, especially at the neuromuscular junction. Knockdown experiments of zbtb42 in zebrafish consistently resulted in grossly abnormal skeletal muscle development and myofibrillar disorganization at the microscopic level. This severe muscular phenotype is successfully rescued with overexpression of the human wild-type ZBTB42 gene, but not with the mutant form of ZBTB42 that models the human missense change. Our data assign a novel muscular developmental phenotype to ZBTB42 in vertebrates and establish a new LCCS6 type caused by ZBTB42 mutation.
Collapse
Affiliation(s)
- Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Laura L Smith
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Eissa Faqeih
- Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia and
| | - Jawahir Mohamed
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Vandana A Gupta
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA,
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia, Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| |
Collapse
|
58
|
Shaheen R, Rahbeeni Z, Alhashem A, Faqeih E, Zhao Q, Xiong Y, Almoisheer A, Al-Qattan SM, Almadani HA, Al-Onazi N, Al-Baqawi BS, Saleh MA, Alkuraya FS. Neu-Laxova syndrome, an inborn error of serine metabolism, is caused by mutations in PHGDH. Am J Hum Genet 2014; 94:898-904. [PMID: 24836451 DOI: 10.1016/j.ajhg.2014.04.015] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 04/28/2014] [Indexed: 11/16/2022] Open
Abstract
Neu-Laxova syndrome (NLS) is a rare autosomal-recessive disorder characterized by severe fetal growth restriction, microcephaly, a distinct facial appearance, ichthyosis, skeletal anomalies, and perinatal lethality. The pathogenesis of NLS remains unclear despite extensive clinical and pathological phenotyping of the >70 affected individuals reported to date, emphasizing the need to identify the underlying genetic etiology, which remains unknown. In order to identify the cause of NLS, we conducted a positional-mapping study combining autozygosity mapping and whole-exome sequencing in three consanguineous families affected by NLS. Surprisingly, the NLS-associated locus identified in this study was solved at the gene level to reveal mutations in PHGDH, which is known to be mutated in individuals with microcephaly and developmental delay. PHGDH encodes the first enzyme in the phosphorylated pathway of de novo serine synthesis, and complete deficiency of its mouse ortholog recapitulates many of the key features of NLS. This study shows that NLS represents the extreme end of a known inborn error of serine metabolism and highlights the power of genomic sequencing in revealing the unsuspected allelic nature of apparently distinct clinical entities.
Collapse
Affiliation(s)
- Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh 11159, Saudi Arabia
| | - Eissa Faqeih
- Department of Pediatrics, King Fahad Medical City, Riyadh 59046, Saudi Arabia
| | - Qi Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Agaadir Almoisheer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Sarah M Al-Qattan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Halima A Almadani
- Pediatric metabolic laboratory, Prince Sultan Military Medical City, Riyadh 11159, Saudi Arabia
| | - Noufa Al-Onazi
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh 11159, Saudi Arabia
| | - Badi S Al-Baqawi
- Maternal Fetal Department, Women's Specialist Hospital, King Fahad Medical City, Riyadh 59046, Saudi Arabia
| | - Mohammad Ali Saleh
- Department of Pediatrics, King Fahad Medical City, Riyadh 59046, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia.
| |
Collapse
|
59
|
Patel N, Khan AO, Mansour A, Mohamed JY, Al-Assiri A, Haddad R, Jia X, Xiong Y, Mégarbané A, Traboulsi EI, Alkuraya FS. Mutations in ASPH cause facial dysmorphism, lens dislocation, anterior-segment abnormalities, and spontaneous filtering blebs, or Traboulsi syndrome. Am J Hum Genet 2014; 94:755-9. [PMID: 24768550 DOI: 10.1016/j.ajhg.2014.04.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 04/02/2014] [Indexed: 11/15/2022] Open
Abstract
We have previously described a syndrome characterized by facial dysmorphism, lens dislocation, anterior-segment abnormalities, and spontaneous filtering blebs (FDLAB, or Traboulsi syndrome). In view of the consanguineous nature of the affected families and the likely autosomal-recessive inheritance pattern of this syndrome, we undertook autozygosity mapping and whole-exome sequencing to identify ASPH as the disease locus, in which we identified two homozygous mutations. ASPH encodes aspartyl/asparaginyl β-hydroxylase (ASPH), which has been found to hydroxylate aspartic acid and asparagine residues on epidermal growth factor (EGF)-domain-containing proteins. The truncating and missense mutations we identified are predicted to severely impair the enzymatic function of ASPH, which suggests a possible link to other forms of ectopia lentis given that many of the genes implicated in this phenotype encode proteins that harbor EGF domains. Developmental analysis of Asph revealed an expression pattern consistent with the proposed link to the human syndrome. Indeed, Asph-knockout mice had a foreshortened snout, which corresponds to the facial abnormalities in individuals with Traboulsi syndrome. These data support a genetic basis for a syndromic form of ectopia lentis and the role of aspartyl hydroxylation in human development.
Collapse
Affiliation(s)
- Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Arif O Khan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia; Division of Pediatric Ophthalmology, King Khaled Eye Specialist Hospital, Riyadh 11462, Saudi Arabia
| | - Ahmad Mansour
- Department of Ophthalmology, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Jawahir Y Mohamed
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Abdullah Al-Assiri
- Division of Anterior Segment, King Khaled Eye Specialist Hospital, Riyadh 11462, Saudi Arabia
| | - Randa Haddad
- Department of Ophthalmology, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Xiaofei Jia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - André Mégarbané
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University, Beirut 1104-2020, Lebanon
| | - Elias I Traboulsi
- Center for Genetic Eye Diseases, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia.
| |
Collapse
|
60
|
Aldahmesh MA, Li Y, Alhashem A, Anazi S, Alkuraya H, Hashem M, Awaji AA, Sogaty S, Alkharashi A, Alzahrani S, Al Hazzaa SA, Xiong Y, Kong S, Sun Z, Alkuraya FS. IFT27, encoding a small GTPase component of IFT particles, is mutated in a consanguineous family with Bardet-Biedl syndrome. Hum Mol Genet 2014; 23:3307-15. [PMID: 24488770 DOI: 10.1093/hmg/ddu044] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is an autosomal recessive ciliopathy with multisystem involvement. So far, 18 BBS genes have been identified and the majority of them are essential for the function of BBSome, a protein complex involved in transporting membrane proteins into and from cilia. Yet defects in the identified genes cannot account for all the BBS cases. The genetic heterogeneity of this disease poses significant challenge to the identification of additional BBS genes. In this study, we coupled human genetics with functional validation in zebrafish and identified IFT27 as a novel BBS gene (BBS19). This is the first time an intraflagellar transport (IFT) gene is implicated in the pathogenesis of BBS, highlighting the genetic complexity of this disease.
Collapse
Affiliation(s)
| | | | - Amal Alhashem
- Deparment of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | - Hisham Alkuraya
- Department of Ophthalmology, College of Medicine, Imam Muhammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | | | - Ali A Awaji
- Department of Pediatrics, King Fahad Central Hospital, Jazan, Saudi Arabia
| | - Sameera Sogaty
- Department of Medical Genetics, King Fahad General Hospital, Jeddah, Saudi Arabia and
| | - Abdullah Alkharashi
- Deparment of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Saeed Alzahrani
- Department of Pediatric Nephrology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Selwa A Al Hazzaa
- Department of Ophthalmology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia Department of Ophthalmology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | | | - Fowzan S Alkuraya
- Department of Genetics and Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| |
Collapse
|
61
|
Alsalem AB, Halees AS, Anazi S, Alshamekh S, Alkuraya FS. Autozygome sequencing expands the horizon of human knockout research and provides novel insights into human phenotypic variation. PLoS Genet 2013; 9:e1004030. [PMID: 24367280 PMCID: PMC3868571 DOI: 10.1371/journal.pgen.1004030] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 10/31/2013] [Indexed: 11/19/2022] Open
Abstract
The use of autozygosity as a mapping tool in the search for autosomal recessive disease genes is well established. We hypothesized that autozygosity not only unmasks the recessiveness of disease causing variants, but can also reveal natural knockouts of genes with less obvious phenotypic consequences. To test this hypothesis, we exome sequenced 77 well phenotyped individuals born to first cousin parents in search of genes that are biallelically inactivated. Using a very conservative estimate, we show that each of these individuals carries biallelic inactivation of 22.8 genes on average. For many of the 169 genes that appear to be biallelically inactivated, available data support involvement in modulating metabolism, immunity, perception, external appearance and other phenotypic aspects, and appear therefore to contribute to human phenotypic variation. Other genes with biallelic inactivation may contribute in yet unknown mechanisms or may be on their way to conversion into pseudogenes due to true recent dispensability. We conclude that sequencing the autozygome is an efficient way to map the contribution of genes to human phenotypic variation that goes beyond the classical definition of disease.
Collapse
Affiliation(s)
- Ahmed B. Alsalem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Internal Medicine, College of Medicine, King Saud bin-Abdul-Aziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Anason S. Halees
- Molecular Biomedicine Program, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shamsa Anazi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shomoukh Alshamekh
- Department of Ophthalmology, King Abdul-Aziz University Hospital, King Saud University, Riyadh, Saudi Arabia
| | - Fowzan S. Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| |
Collapse
|
62
|
MYSM1 is mutated in a family with transient transfusion-dependent anemia, mild thrombocytopenia, and low NK- and B-cell counts. Blood 2013; 122:3844-5. [DOI: 10.1182/blood-2013-09-527127] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
63
|
Helm BM, Langley K, Spangler B, Vergano S. Three clinical experiences with SNP array results consistent with parental incest: a narrative with lessons learned. J Genet Couns 2013; 23:489-95. [PMID: 24222483 DOI: 10.1007/s10897-013-9669-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 10/31/2013] [Indexed: 02/05/2023]
Abstract
Single nucleotide polymorphism microarrays have the ability to reveal parental consanguinity which may or may not be known to healthcare providers. Consanguinity can have significant implications for the health of patients and for individual and family psychosocial well-being. These results often present ethical and legal dilemmas that can have important ramifications. Unexpected consanguinity can be confounding to healthcare professionals who may be unprepared to handle these results or to communicate them to families or other appropriate representatives. There are few published accounts of experiences with consanguinity and SNP arrays. In this paper we discuss three cases where molecular evidence of parental incest was identified by SNP microarray. We hope to further highlight consanguinity as a potential incidental finding, how the cases were handled by the clinical team, and what resources were found to be most helpful. This paper aims to contribute further to professional discourse on incidental findings with genomic technology and how they were addressed clinically. These experiences may provide some guidance on how others can prepare for these findings and help improve practice. As genetic and genomic testing is utilized more by non-genetics providers, we also hope to inform about the importance of engaging with geneticists and genetic counselors when addressing these findings.
Collapse
Affiliation(s)
- Benjamin M Helm
- Department of Medical Genetics and Metabolism, Children's Hospital of the King's Daughters/Eastern Virginia Medical School, 601 Children's Lane, 2nd Floor Pediatrics, Norfolk, VA, 23507, USA,
| | | | | | | |
Collapse
|
64
|
Campbell CD, Eichler EE. Properties and rates of germline mutations in humans. Trends Genet 2013; 29:575-84. [PMID: 23684843 PMCID: PMC3785239 DOI: 10.1016/j.tig.2013.04.005] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/05/2013] [Accepted: 04/18/2013] [Indexed: 11/25/2022]
Abstract
All genetic variation arises via new mutations; therefore, determining the rate and biases for different classes of mutation is essential for understanding the genetics of human disease and evolution. Decades of mutation rate analyses have focused on a relatively small number of loci because of technical limitations. However, advances in sequencing technology have allowed for empirical assessments of genome-wide rates of mutation. Recent studies have shown that 76% of new mutations originate in the paternal lineage and provide unequivocal evidence for an increase in mutation with paternal age. Although most analyses have focused on single nucleotide variants (SNVs), studies have begun to provide insight into the mutation rate for other classes of variation, including copy number variants (CNVs), microsatellites, and mobile element insertions (MEIs). Here, we review the genome-wide analyses for the mutation rate of several types of variants and suggest areas for future research.
Collapse
Affiliation(s)
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Howard Hughes Medical Institute, Seattle, WA 98195
| |
Collapse
|
65
|
Khan AO, Aldahmesh MA, Noor J, Salem A, Alkuraya FS. Lens subluxation and retinal dysfunction in a girl with homozygous VSX2 mutation. Ophthalmic Genet 2013; 36:8-13. [PMID: 24001013 DOI: 10.3109/13816810.2013.827217] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE To describe a unique lens subluxation phenotype in a child from a consanguineous family and to determine its genetic basis. METHODS Ophthalmologic examination (including ocular biometry and electroretinography [ERG] for the proband) and autozygosity-analysis-guided exome sequencing for the family; confirmatory candidate gene sequencing in the family and ethnically matched controls. RESULTS An otherwise healthy 3-year-old Saudi Arabian girl with poor vision since birth had smooth irides, lens subluxation, cone-rod dysfunction, and high myopia - features resembling Knobloch syndrome but differing in regard to direction of lens subluxation (superior rather than temporal) and the pattern of chorioretinal atrophy (without vitreous condensations or distinct macular atrophy). Autozygome-guided exome sequencing revealed the girl to harbor a homozygous exon 5 mutation in the ocular transcription factor gene visual homeobox 2 (VSX2) [c.773delA; p.Lys258SerfsX44] that was heterozygous in the unaffected brother and parents and absent in 100 healthy ethnically matched controls and on-line databases. Previously reported VSX2 mutations have affected the DNA-binding domains and only been associated with microphthalmia. Unlike previously reported mutations, the current VSX2 mutation is downstream to the protein's DNA binding domains. CONCLUSIONS The phenotype of this girl is unique and suggests a normal regulatory role for VSX2 in iris, zonule, and cone-rod development. For a consanguineous family with suspected recessive ocular disease but without a clear candidate gene, autozygome-guided exome analysis is a powerful technique, even when only a single patient is affected.
Collapse
Affiliation(s)
- Arif O Khan
- Division of Pediatric Ophthalmology, King Khaled Eye Specialist Hospital , Riyadh , Saudi Arabia
| | | | | | | | | |
Collapse
|
66
|
Aldahmesh M, Khan A, Alkuraya H, Adly N, Anazi S, Al-Saleh A, Mohamed J, Hijazi H, Prabakaran S, Tacke M, Al-Khrashi A, Hashem M, Reinheckel T, Assiri A, Alkuraya F. Mutations in LRPAP1 are associated with severe myopia in humans. Am J Hum Genet 2013; 93:313-20. [PMID: 23830514 DOI: 10.1016/j.ajhg.2013.06.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/30/2013] [Accepted: 06/03/2013] [Indexed: 10/26/2022] Open
Abstract
Myopia is an extremely common eye disorder but the pathogenesis of its isolated form, which accounts for the overwhelming majority of cases, remains poorly understood. There is strong evidence for genetic predisposition to myopia, but determining myopia genetic risk factors has been difficult to achieve. We have identified Mendelian forms of myopia in four consanguineous families and implemented exome/autozygome analysis to identify homozygous truncating variants in LRPAP1 and CTSH as the likely causal mutations. LRPAP1 encodes a chaperone of LRP1, which is known to influence TGF-β activity. Interestingly, we observed marked deficiency of LRP1 and upregulation of TGF-β in cells from affected individuals, the latter being consistent with available data on the role of TGF-β in the remodeling of the sclera in myopia and the high frequency of myopia in individuals with Marfan syndrome who characteristically have upregulation of TGF-β signaling. CTSH, on the other hand, encodes a protease and we show that deficiency of the murine ortholog results in markedly abnormal globes consistent with the observed human phenotype. Our data highlight a role for LRPAP1 and CTSH in myopia genetics and demonstrate the power of Mendelian forms in illuminating new molecular mechanisms that may be relevant to common phenotypes.
Collapse
|
67
|
The application of next-generation sequencing in the autozygosity mapping of human recessive diseases. Hum Genet 2013; 132:1197-211. [PMID: 23907654 DOI: 10.1007/s00439-013-1344-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 07/20/2013] [Indexed: 02/08/2023]
Abstract
Autozygosity, or the inheritance of two copies of an ancestral allele, has the potential to not only reveal phenotypes caused by biallelic mutations in autosomal recessive genes, but to also facilitate the mapping of such mutations by flagging the surrounding haplotypes as tractable runs of homozygosity (ROH), a process known as autozygosity mapping. Since SNPs replaced microsatellites as markers for the purpose of genomewide identification of ROH, autozygosity mapping of Mendelian genes has witnessed a significant acceleration. Historically, successful mapping traditionally required favorable family structure that permits the identification of an autozygous interval that is amenable to candidate gene selection and confirmation by Sanger sequencing. This requirement presented a major bottleneck that hindered the utilization of simplex cases and many multiplex families with autosomal recessive phenotypes. However, the advent of next-generation sequencing that enables massively parallel sequencing of DNA has largely bypassed this bottleneck and thus ushered in an era of unprecedented pace of Mendelian disease gene discovery. The ability to identify a single causal mutation among a massive number of variants that are uncovered by next-generation sequencing can be challenging, but applying autozygosity as a filter can greatly enhance the enrichment process and its throughput. This review will discuss the power of combining the best of both techniques in the mapping of recessive disease genes and offer some tips to troubleshoot potential limitations.
Collapse
|
68
|
Khan AO, Aldahmesh MA, Mohamed JY, Hijazi H, Alkuraya FS. Complete Aniridia with Central Keratopathy and Congenital Glaucoma is aCYP1B1-related Phenotype. Ophthalmic Genet 2013; 35:187-9. [DOI: 10.3109/13816810.2013.804096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
69
|
Khan AO, Aldahmesh MA, Abu-Safieh L, Alkuraya FS. Childhood cone-rod dystrophy with macular cystic degeneration from recessive CRB1 mutation. Ophthalmic Genet 2013; 35:130-7. [PMID: 23767994 DOI: 10.3109/13816810.2013.804097] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE To describe three siblings with childhood cone-rod dystrophy and macular cystic degeneration in a family with apparently variable phenotypes of CRB1-related recessive retinal dystrophy. METHODS Ophthalmologic examination (including electroretinography (ERG), ocular coherence tomography (OCT), and intravenous fluorescein angiography when possible) and homozygosity analysis guided candidate gene testing. RESULTS When the proband was evaluated at 7 years old for progressive visual loss, fundus exam was unremarkable (including no macular thickening clinically or by OCT) but ERG revealed cone-rod dysfunction with an electronegative waveform. Four years later repeat examination was significant for bilateral macular cystic degeneration and immediate family members were evaluated. Both the older sister (15 years old) and the younger brother (7 years old) had cone-rod dystrophy with macular cystic degeneration. Both the father (45 years old) and mother (35 years old) had had early adult-onset nyctalopia with later eventual loss of central vision; examination revealed dystrophic retinas with mostly peripheral clumped and/or nummular pigment and macular atrophy. ERG for both the older sister and younger brother confirmed cone-rod dysfunction (without an electronegative waveform) and was non-recordable for both the parents. Homozygosity analysis guided candidate gene analysis and confirmatory Sanger sequencing for the family uncovered a homozygous CRB1 mutation (c.80G > T [p.Cys27Phe]) in affected family members. CONCLUSIONS The phenotypic spectrum of recessive CRB1 mutation includes childhood cone-rod dystrophy with macular cystic degeneration and the associated ERG can be electronegative.
Collapse
Affiliation(s)
- Arif O Khan
- Division of Pediatric Ophthalmology, King Khaled Eye Specialist Hospital , Riyadh , Saudi Arabia
| | | | | | | |
Collapse
|
70
|
Anazi S, Al-Sabban E, Alkuraya FS. Gonadal mosaicism as a rare cause of autosomal recessive inheritance. Clin Genet 2013; 85:278-81. [PMID: 23551117 DOI: 10.1111/cge.12156] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 03/27/2013] [Accepted: 03/27/2013] [Indexed: 11/26/2022]
Abstract
Autosomal recessive diseases are typically caused by the biparental inheritance of familial mutant alleles. Unusual mechanisms by which the recessiveness of a mutant allele is unmasked include uniparental isodisomy and the occurrence of a de novo chromosomal rearrangement that disrupts the other allele. Gonadal mosaicism is a condition in which a postfertilization mutation is confined to the gamete precursors and is not detected in somatic tissues. Gonadal mosaicism is known to give the impression of autosomal recessive inheritance when recurrence of an autosomal-dominant condition among offspring of phenotypically normal parents is observed. Here, we report an extremely rare event in which maternal gonadal mosaicism for a recessive mutation in COL4A4 caused the recurrence of Alport syndrome within a consanguineous family. Such rare occurrence should be taken into account when analyzing pedigrees both for clinical and research purposes.
Collapse
|
71
|
Use of whole exome and genome sequencing in the identification of genetic causes of primary immunodeficiencies. Curr Opin Allergy Clin Immunol 2013; 12:623-8. [PMID: 23095910 DOI: 10.1097/aci.0b013e3283588ca6] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW This review discusses the strengths and challenges of using whole genome sequencing (WGS)/whole exome sequencing (WES) for identifying novel genetic causes of primary immunodeficiencies. RECENT FINDINGS WGS permits comprehensive sequencing of introns and exons, whereas WES allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS/WES. SUMMARY WGS/WES is a powerful screening tool with great potential to identify genetic causes of primary immunodeficiencies for research and clinical applications. To use WGS/WES effectively, it is necessary to understand how to filter the sequencing data and to realize its limitations as well as its strengths.
Collapse
|
72
|
Alkuraya FS. Impact of new genomic tools on the practice of clinical genetics in consanguineous populations: the Saudi experience. Clin Genet 2013; 84:203-8. [DOI: 10.1111/cge.12131] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 02/19/2013] [Accepted: 02/19/2013] [Indexed: 12/29/2022]
|
73
|
Alkuraya FS. Discovery of rare homozygous mutations from studies of consanguineous pedigrees. ACTA ACUST UNITED AC 2013; Chapter 6:Unit6.12. [PMID: 23074070 DOI: 10.1002/0471142905.hg0612s75] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The unmasking of recessive mutations by virtue of biparental inheritance of the same ancestral haplotype on which they reside (autozygosity) has provided human geneticists with one of their most powerful tools in unraveling the genetic basis of autosomal recessive disorders. This has historically been achieved by tracking the blocks of homozygosity as surrogates of autozygosity using polymorphic microsatellite markers. Mapping the entire set of autozygous blocks per individual (autozygome) at high resolution became possible with the advent of high-density SNP arrays. The more recent availability of next-generation sequencing has markedly accelerated the rate at which rare recessive mutations are identified by obviating the need to prioritize genes for sequencing within candidate autozygous loci. This unit will review the individual and combined use of these techniques in the context of mapping novel recessive disease genes, as well as potential pitfalls and recommended solutions.
Collapse
Affiliation(s)
- Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| |
Collapse
|
74
|
Zahrani F, Aldahmesh M, Alshammari M, Al-Hazzaa SA, Alkuraya F. Mutations in c12orf57 cause a syndromic form of colobomatous microphthalmia. Am J Hum Genet 2013; 92:387-91. [PMID: 23453665 DOI: 10.1016/j.ajhg.2013.01.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 11/12/2012] [Accepted: 01/02/2013] [Indexed: 10/27/2022] Open
Abstract
Microphthalmia is an important developmental eye disorder. Although mutations in several genes have been linked to this condition, they only account for a minority of cases. We performed autozygome analysis and exome sequencing on a multiplex consanguineous family in which colobomatous microphthalmia is associated with profound global developmental delay, intractable seizures, and corpus callosum abnormalities, and we identified a homozygous truncating mutation in C12orf57 [c.1A>G; p.Met1?]. In a simplex case with a similar phenotype, we identified compound heterozygosity for the same mutation and another missense mutation [c.152T>A; p.Leu51Gln]. Little is known about C12orf57 but we show that it is expressed in several mouse tissues, including the eye and brain. Our data strongly implicate mutations in C12orf57 in the pathogenesis of a clinically distinct autosomal-recessive syndromic form of colobomatous microphthalmia.
Collapse
|
75
|
Kijas JW. Detecting regions of homozygosity to map the cause of recessively inherited disease. Methods Mol Biol 2013; 1019:331-45. [PMID: 23756898 DOI: 10.1007/978-1-62703-447-0_14] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Homozygosity is a component of genetic patterning that can be used to search for the cause of genetic disease. In this chapter, methods are presented to analyze SNP data for the presence of homozygosity. Two exercises demonstrate methods to define runs of homozygosity, to identify shared homozygosity between individuals, and to evaluate the results in light of the expectations of a recessively inherited genetic disorder. An example dataset is used to aid in data interpretation.
Collapse
Affiliation(s)
- James W Kijas
- Division of Animal, Food, and Health Sciences, CSIRO, Queensland Bioscience Precinct, Brisbane, QLD, Australia
| |
Collapse
|
76
|
Abu-Safieh L, Alrashed M, Anazi S, Alkuraya H, Khan AO, Al-Owain M, Al-Zahrani J, Al-Abdi L, Hashem M, Al-Tarimi S, Sebai MA, Shamia A, Ray-Zack MD, Nassan M, Al-Hassnan ZN, Rahbeeni Z, Waheeb S, Alkharashi A, Abboud E, Al-Hazzaa SAF, Alkuraya FS. Autozygome-guided exome sequencing in retinal dystrophy patients reveals pathogenetic mutations and novel candidate disease genes. Genome Res 2012; 23:236-47. [PMID: 23105016 PMCID: PMC3561865 DOI: 10.1101/gr.144105.112] [Citation(s) in RCA: 209] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Retinal dystrophy (RD) is a heterogeneous group of hereditary diseases caused by loss of photoreceptor function and contributes significantly to the etiology of blindness globally but especially in the industrialized world. The extreme locus and allelic heterogeneity of these disorders poses a major diagnostic challenge and often impedes the ability to provide a molecular diagnosis that can inform counseling and gene-specific treatment strategies. In a large cohort of nearly 150 RD families, we used genomic approaches in the form of autozygome-guided mutation analysis and exome sequencing to identify the likely causative genetic lesion in the majority of cases. Additionally, our study revealed six novel candidate disease genes (C21orf2, EMC1, KIAA1549, GPR125, ACBD5, and DTHD1), two of which (ACBD5 and DTHD1) were observed in the context of syndromic forms of RD that are described for the first time.
Collapse
Affiliation(s)
- Leen Abu-Safieh
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
77
|
Kheradmand Kia S, Verbeek E, Engelen E, Schot R, Poot R, de Coo I, Lequin M, Poulton C, Pourfarzad F, Grosveld F, Brehm A, de Wit M, Oegema R, Dobyns W, Verheijen F, Mancini G. RTTN mutations link primary cilia function to organization of the human cerebral cortex. Am J Hum Genet 2012; 91:533-40. [PMID: 22939636 DOI: 10.1016/j.ajhg.2012.07.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/09/2012] [Accepted: 07/11/2012] [Indexed: 10/28/2022] Open
Abstract
Polymicrogyria is a malformation of the developing cerebral cortex caused by abnormal organization and characterized by many small gyri and fusion of the outer molecular layer. We have identified autosomal-recessive mutations in RTTN, encoding Rotatin, in individuals with bilateral diffuse polymicrogyria from two separate families. Rotatin determines early embryonic axial rotation, as well as anteroposterior and dorsoventral patterning in the mouse. Human Rotatin has recently been identified as a centrosome-associated protein. The Drosophila melanogaster homolog of Rotatin, Ana3, is needed for structural integrity of centrioles and basal bodies and maintenance of sensory neurons. We show that Rotatin colocalizes with the basal bodies at the primary cilium. Cultured fibroblasts from affected individuals have structural abnormalities of the cilia and exhibit downregulation of BMP4, WNT5A, and WNT2B, which are key regulators of cortical patterning and are expressed at the cortical hem, the cortex-organizing center that gives rise to Cajal-Retzius (CR) neurons. Interestingly, we have shown that in mouse embryos, Rotatin colocalizes with CR neurons at the subpial marginal zone. Knockdown experiments in human fibroblasts and neural stem cells confirm a role for RTTN in cilia structure and function. RTTN mutations therefore link aberrant ciliary function to abnormal development and organization of the cortex in human individuals.
Collapse
|
78
|
Regions of homozygosity identified by SNP microarray analysis aid in the diagnosis of autosomal recessive disease and incidentally detect parental blood relationships. Genet Med 2012; 15:70-8. [PMID: 22858719 DOI: 10.1038/gim.2012.94] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
PURPOSE The purpose of this study was to document the ability of single-nucleotide polymorphism microarray to identify copy-neutral regions of homozygosity, demonstrate clinical utility of regions of homozygosity, and discuss ethical/legal implications when regions of homozygosity are associated with a parental blood relationship. METHODS Study data were compiled from consecutive samples sent to our clinical laboratory over a 3-year period. A cytogenetics database identified patients with at least two regions of homozygosity >10 Mb on two separate chromosomes. A chart review was conducted on patients who met the criteria. RESULTS Of 3,217 single-nucleotide polymorphism microarrays, 59 (1.8%) patients met inclusion criteria. The percentage of homozygosity ranged from 0.9 to 30.1%, indicating parental relationships from distant to first-degree relatives. First-degree kinship was suspected in the parents of at least 11 patients with regions of homozygosity covering >21.3% of their autosome. In four patients from two families, homozygosity mapping discovered a candidate gene that was sequenced to identify a clinically significant mutation. CONCLUSION This study demonstrates clinical utility in the identification of regions of homozygosity, as these regions may aid in diagnosis of the patient. This study establishes the need for careful reporting, thorough pretest counseling, and careful electronic documentation, as microarray has the capability of detecting previously unknown/unreported relationships.
Collapse
|
79
|
Alangari A, Alsultan A, Adly N, Massaad MJ, Kiani IS, Aljebreen A, Raddaoui E, Almomen AK, Al-Muhsen S, Geha RS, Alkuraya FS. LPS-responsive beige-like anchor (LRBA) gene mutation in a family with inflammatory bowel disease and combined immunodeficiency. J Allergy Clin Immunol 2012; 130:481-8.e2. [PMID: 22721650 PMCID: PMC3582381 DOI: 10.1016/j.jaci.2012.05.043] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Revised: 05/29/2012] [Accepted: 05/29/2012] [Indexed: 12/17/2022]
Abstract
BACKGROUND Clinical immunology has traditionally relied on accurate phenotyping of the patient's immune dysfunction for the identification of a candidate gene or genes for sequencing and molecular confirmation. Although this is also true for other branches of medicine, the marked variability in immune-related phenotypes and the highly complex network of molecules that confer normal host immunity are challenges that clinical immunologists often face in their quest to establish a specific genetic diagnosis. OBJECTIVE We sought to identify the underlying genetic cause in a consanguineous family with chronic inflammatory bowel disease-like disorder and combined immunodeficiency. METHODS We performed exome sequencing followed by autozygome filtration. RESULTS A truncating mutation in LPS-responsive beige-like anchor (LRBA), which abolished protein expression, was identified as the most likely candidate variant in this family. CONCLUSION The combined exome sequencing and autozygosity mapping approach is a powerful tool in the study of atypical immune dysfunctions. We identify LRBA as a novel immunodeficiency candidate gene the precise role of which in the immune system requires future studies.
Collapse
Affiliation(s)
- Abdullah Alangari
- Departments of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Abdulrahman Alsultan
- Departments of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Nouran Adly
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh
| | - Michel J. Massaad
- Departments of Pathology, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Iram Shakir Kiani
- Departments of Internal Medicine, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Abdulrahman Aljebreen
- Departments of Internal Medicine, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Emad Raddaoui
- Departments of Pathology, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Abdul-Kareem Almomen
- Departments of Internal Medicine, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Saleh Al-Muhsen
- Departments of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Raif S. Geha
- Department of the Division of Immunology, Children’s Hospital Boston and Harvard Medical School, Boston
| | - Fowzan S. Alkuraya
- Departments of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh
| |
Collapse
|
80
|
Khan AO. Microcornea with myopic chorioretinal atrophy, telecanthus and posteriorly-rotated ears: a distinct clinical syndrome. Ophthalmic Genet 2012; 33:196-9. [DOI: 10.3109/13816810.2012.681097] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
81
|
Colorectal cancer risk is not associated with increased levels of homozygosity in Saudi Arabia. Genet Med 2012; 14:720-728. [PMID: 22481135 DOI: 10.1038/gim.2012.27] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Purpose:Runs of homozygosity (ROHs) represent a measure of the extent of autozygosity and are correlated with the extent of inbreeding. Recently, it has been suggested that ROHs may contribute to the risk of colorectal cancer (CRC). The high rate of consanguinity and CRC in the Saudi population prompted us to test the role of autozygosity in the CRC risk.Methods:We compared 48 Saudi CRC patients to 100 ethnically matched controls, processed on the Affymetrix 250K StyI SNP GeneChip platform and analyzed using the plink package.Results:We could find no evidence of a significant relationship between autozygosity and CRC risk.Conclusion:The negative results in our study add additional significance to what has been previously reported in literature, as this is the first study to address these questions in an inbred population. Our subgroup analysis of patients with microsatellite unstable-positive tumors as compared with other groups did not significantly change our results. Although these results do not rule out the presence of recessively acting CRC-predisposing genes in a small percentage of patients, which our relatively small sample size could not capture, they suggest that such genes are unlikely to account for the disturbingly high incidence of CRC in our consanguineous population.Genet Med advance online publication 5 April 2012.
Collapse
|
82
|
Khalak HG, Wakil SM, Imtiaz F, Ramzan K, Baz B, Almostafa A, Hagos S, Alzahrani F, Abu-Dhaim N, Abu Safieh L, Al-Jbali L, Al-Hamed MS, Monies D, Aldahmesh M, Al-Dosari MS, Kaya N, Shamseldin H, Shaheen R, Al-Rashed M, Hashem M, Al-Tassan N, Meyer B, Alazami AM, Alkuraya FS. Autozygome maps dispensable DNA and reveals potential selective bias against nullizygosity. Genet Med 2012; 14:515-9. [PMID: 22241088 DOI: 10.1038/gim.2011.28] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Copy number variants are an important source of human genome diversity. The widespread distribution of hemizygous copy number variants in the DNA of healthy humans suggests that haploinsufficiency is largely tolerated. However, little is known about the extent to which corresponding nullizygosity (two-copy deletion) is similarly tolerated. METHODS We analyzed a cohort of first cousin unions to enrich for shared parental hemizygous events and tested their Mendelian inheritance in offspring. RESULTS Analysis of autozygous DNA blocks (autozygome) in the offspring not only proved an efficient method of mapping "dispensable" DNA but also revealed potential selective bias against the occurrence of nullizygous changes. This bias was not restricted to genic copy number variants and was not accounted for by a high rate of miscarriages. CONCLUSIONS The autozygome is an efficient way to map dispensable segments of DNA and may reveal selective bias against nullizygosity in healthy individuals.
Collapse
Affiliation(s)
- Hanif G Khalak
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
83
|
Recessive mutations in ELOVL4 cause ichthyosis, intellectual disability, and spastic quadriplegia. Am J Hum Genet 2011; 89:745-50. [PMID: 22100072 DOI: 10.1016/j.ajhg.2011.10.011] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 10/20/2011] [Accepted: 10/26/2011] [Indexed: 12/21/2022] Open
Abstract
Very-long-chain fatty acids (VLCFAs) play important roles in membrane structure and cellular signaling, and their contribution to human health is increasingly recognized. Fatty acid elongases catalyze the first and rate-limiting step in VLCFA synthesis. Heterozygous mutations in ELOVL4, the gene encoding one of the elongases, are known to cause macular degeneration in humans and retinal abnormalities in mice. However, biallelic ELOVL4 mutations have not been observed in humans, and murine models with homozygous mutations die within hours of birth as a result of a defective epidermal water barrier. Here, we report on two human individuals with recessive ELOVL4 mutations revealed by a combination of autozygome analysis and exome sequencing. These individuals exhibit clinical features of ichthyosis, seizures, mental retardation, and spasticity-a constellation that resembles Sjögren-Larsson syndrome (SLS) but presents a more severe neurologic phenotype. Our findings identify recessive mutations in ELOVL4 as the cause of a neuro-ichthyotic disease and emphasize the importance of VLCFA synthesis in brain and cutaneous development.
Collapse
|
84
|
Kearney HM, Kearney JB, Conlin LK. Diagnostic Implications of Excessive Homozygosity Detected by SNP-Based Microarrays: Consanguinity, Uniparental Disomy, and Recessive Single-Gene Mutations. Clin Lab Med 2011; 31:595-613, ix. [DOI: 10.1016/j.cll.2011.08.003] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
85
|
Loss-of-function variant in DNASE1L3 causes a familial form of systemic lupus erythematosus. Nat Genet 2011; 43:1186-8. [PMID: 22019780 DOI: 10.1038/ng.975] [Citation(s) in RCA: 306] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 09/19/2011] [Indexed: 02/03/2023]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease that causes substantial morbidity. As is typical for many other multifactorial disorders, much of the heritability of SLE remains unknown. We identified a rare autosomal recessive form of SLE, in which autozygome analysis revealed a null mutation in the DNASE1L3 gene. The DNASE1L3-related SLE we describe was always pediatric in onset and correlated with a high frequency of lupus nephritis. Our findings confirm the critical role of impaired clearance of degraded DNA in SLE pathogenesis.
Collapse
|
86
|
Shaheen R, Faqeih E, Sunker A, Morsy H, Al-Sheddi T, Shamseldin H, Adly N, Hashem M, Alkuraya. F. Recessive mutations in DOCK6, encoding the guanidine nucleotide exchange factor DOCK6, lead to abnormal actin cytoskeleton organization and Adams-Oliver syndrome. Am J Hum Genet 2011; 89:328-33. [PMID: 21820096 DOI: 10.1016/j.ajhg.2011.07.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 07/13/2011] [Accepted: 07/17/2011] [Indexed: 12/26/2022] Open
Abstract
Adams-Oliver syndrome (AOS) is defined by the combination of aplasia cutis congenita (ACC) and terminal transverse limb defects (TTLD). It is usually inherited as an autosomal-dominant trait, but autosomal-recessive inheritance has also been documented. In an individual with autosomal-recessive AOS, we combined autozygome analysis with exome sequencing to identify a homozygous truncating mutation in dedicator of cytokinesis 6 gene (DOCK6) which encodes an atypical guanidine exchange factor (GEF) known to activate two members of the Rho GTPase family: Cdc42 and Rac1. Another homozygous truncating mutation was identified upon targeted sequencing of DOCK6 in an unrelated individual with AOS. Consistent with the established role of Cdc42 and Rac1 in the organization of the actin cytoskeleton, we demonstrate a cellular phenotype typical of a defective actin cytoskeleton in patient cells. These findings, combined with a Dock6 expression profile that is consistent with an AOS phenotype as well as the very recent demonstration of dominant mutations of ARHGAP31 in AOS, establish Cdc42 and Rac1 as key molecules in the pathogenesis of AOS and suggest that other regulators of these Rho GTPase proteins might be good candidates in the quest to define the genetic spectrum of this genetically heterogeneous condition.
Collapse
|
87
|
Alazami AM, Adly N, Al Dhalaan H, Alkuraya FS. A nullimorphic ERLIN2 mutation defines a complicated hereditary spastic paraplegia locus (SPG18). Neurogenetics 2011; 12:333-6. [PMID: 21796390 PMCID: PMC3215864 DOI: 10.1007/s10048-011-0291-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 06/29/2011] [Indexed: 12/14/2022]
Abstract
Hereditary Spastic Paraplegia (HSP) is a clinically and genetically heterogeneous group of neurological disorders that are characterized by progressive spasticity of the lower extremities. We describe an extended consanguineous Saudi family in which HSP is linked to SPG18, a previously reported autosomal recessive locus, and show that it is associated with a nullimorphic deletion of ERLIN2, a component of endoplasmic reticulum associated degradation. This finding adds to the growing diversity of cellular functions that are now known to be involved in the maintenance of the corticospinal tract neurons.
Collapse
Affiliation(s)
- Anas M Alazami
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | | | | |
Collapse
|