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Wei J, Beebe-Dimmer J, Shi Z, Sample C, Yan G, Rifkin AS, Sadeghpour A, Gielzak M, Choi S, Moon D, Zheng SL, Helfand BT, Walsh PC, Xu J, Cooney KA, Isaacs WB. Association of rare, recurrent nonsynonymous variants in the germline of prostate cancer patients of African ancestry. Prostate 2023; 83:454-461. [PMID: 36567534 DOI: 10.1002/pros.24477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Although men of African ancestry (AA) have the highest mortality rate from prostate cancer (PCa), relatively little is known about the germline variants that are associated with PCa risk in AA men. The goal of this study is to systematically evaluate rare, recurrent nonsynonymous variants across the exome for their association with PCa in AA men. METHODS Whole exome sequencing (WES) of germline DNA in two AA PCa patient cohorts of Johns Hopkins Hospital (N = 960) and Wayne State University (N = 747) was performed. All nonsynonymous variants present in both case cohorts, with a carrier rate between 0.5% and 1%, were identified. Their carrier rates were compared with rates from 8128 African/African American (AFR) control subjects from The Genome Aggregation Database (gnomAD) using Fisher's exact test. Significant variants, defined as false discovery rate (FDR) adjusted p-value ≤ 0.05, were further evaluated in AA PCa cases (N = 132) and controls (N = 1184) from the UK Biobank (UKB). RESULTS Two variants reached a pre-specified statistical significance level. The first was p.R14Q in GPRC5C (found in 0.47% of PCa cases and 0.01% of population controls); odds ratio (OR) for PCa was 37.46 (95% confidence interval CI 4.68-299.72), pexact = 7.01E-06, FDR-adjusted p-value = 0.05. The second was p.R511Q in IGF1R (found in 0.53% of PCa cases and 0.01% of population controls); OR for PCa was 21.54 (95%CI 4.65-99.76), pexact = 5.51E-06, FDR-adjusted p-value = 0.05. The mean percentage of African ancestry was similar between variant carriers and noncarriers of each variant, p > 0.05. In the UKB AA men, GPRC5C R14Q was 0.76% and 0.08% in cases and controls, respectively, OR for PCa was 9.00 (95%CI 0.56-145.23), pexact = 0.19. However, IGF1R R511Q was not found in cases or controls. CONCLUSIONS This WES study identified two rare, recurrent nonsynonymous PCa risk-associated variants in AA. Confirmation in additional large populations of AA PCa cases and controls is required.
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Affiliation(s)
- Jun Wei
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Jennifer Beebe-Dimmer
- Barabara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Zhuqing Shi
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Christopher Sample
- Department of Medicine, Duke University School of Medicine and Duke Cancer Institute, Durham, North Carolina, USA
| | - Guifang Yan
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Andrew S Rifkin
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Azita Sadeghpour
- Department of Medicine, Duke University School of Medicine and Duke Cancer Institute, Durham, North Carolina, USA
| | - Marta Gielzak
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Sodam Choi
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - David Moon
- Department of Medicine, Duke University School of Medicine and Duke Cancer Institute, Durham, North Carolina, USA
| | - S Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Brian T Helfand
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
- Department of Surgery, University of Chicago Pritzker School of Medicine, Chicago, Illinois, USA
| | - Patrick C Walsh
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Kathleen A Cooney
- Department of Medicine, Duke University School of Medicine and Duke Cancer Institute, Durham, North Carolina, USA
| | - William B Isaacs
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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Forbes BE, Blyth AJ, Wit JM. Disorders of IGFs and IGF-1R signaling pathways. Mol Cell Endocrinol 2020; 518:111035. [PMID: 32941924 DOI: 10.1016/j.mce.2020.111035] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/02/2020] [Accepted: 09/11/2020] [Indexed: 12/12/2022]
Abstract
The insulin-like growth factor (IGF) system comprises two ligands, IGF-I and IGF-II, that regulate multiple physiological processes, including mammalian development, metabolism and growth, through the type 1 IGF receptor (IGF-1R). The growth hormone (GH)-IGF-I axis is the major regulator of longitudinal growth. IGF-II is expressed in many tissues, notably the placenta, to regulate human pre- and post-natal growth and development. This review provides a brief introduction to the IGF system and summarizes findings from reports arising from recent larger genomic sequencing studies of human genetic mutations in IGF1 and IGF2 and genes of proteins regulating IGF action, namely the IGF-1R, IGF-1R signaling pathway components and the IGF binding proteins (IGFBPs). A perspective on the effect of homozygous mutations on structure and function of the IGFs and IGF-1R is also given and this is related to the effects on growth.
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Affiliation(s)
- Briony E Forbes
- Discipline of Medical Biochemistry, Flinders Health and Medical Research Institute, Flinders University, Australia.
| | - Andrew J Blyth
- Discipline of Medical Biochemistry, Flinders Health and Medical Research Institute, Flinders University, Australia
| | - Jan M Wit
- Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
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3
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Gkourogianni A, Andrade AC, Jonsson B, Segerlund E, Werner‐Sperker A, Horemuzova E, Dahlgren J, Burstedt M, Nilsson O. Pre- and postnatal growth failure with microcephaly due to two novel heterozygous IGF1R mutations and response to growth hormone treatment. Acta Paediatr 2020; 109:2067-2074. [PMID: 32037650 DOI: 10.1111/apa.15218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/21/2020] [Accepted: 02/07/2020] [Indexed: 11/29/2022]
Abstract
AIM To explore the phenotype and response to growth hormone in patients with heterozygous mutations in the insulin-like growth factor I receptor gene (IGF1R). METHODS Children with short stature, microcephaly, born SGA combined with biochemical sign of IGF-I insensitivity were analysed for IGF1R mutations or deletions using Sanger sequencing and Multiple ligation-dependent probe amplification analysis. RESULTS In two families, a novel heterozygous non-synonymous missense IGF1R variant was identified. In family 1, c.3364G > T, p.(Gly1122Cys) was found in the proband and co-segregated perfectly with the phenotype in three generations. In family 2, a de novo variant c.3530G > A, p.(Arg1177His) was detected. Both variants were rare, not present in the GnomAD database. Three individuals carrying IGF1R mutations have received rhGH treatment. The average gain in height SDS during treatment was 0.42 (range: 0.26-0.60) and 0.64 (range: 0.32-0.86) after 1 and 2 years of treatment, respectively. CONCLUSION Our study presents two heterozygous IGF1R mutations causing pre- and postnatal growth failure and microcephaly and also indicates that individuals with heterozygous IGF1R mutations can respond to rhGH treatment. The findings highlight that sequencing of the IGF1R should be considered in children with microcephaly and short stature due to pre- and postnatal growth failure.
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Affiliation(s)
- Alexandra Gkourogianni
- Division of Pediatric Endocrinology Department of Women’s and Children’s Health Karolinska Institutet and University Hospital Stockholm Sweden
- Center for Molecular Medicine Karolinska Institutet and University Hospital Stockholm Sweden
| | - Anenisia C. Andrade
- Division of Pediatric Endocrinology Department of Women’s and Children’s Health Karolinska Institutet and University Hospital Stockholm Sweden
- Center for Molecular Medicine Karolinska Institutet and University Hospital Stockholm Sweden
| | - Björn‐Anders Jonsson
- Department of Medical Biosciences Medical and Clinical Genetics Umeå University Umeå Sweden
| | - Emma Segerlund
- Department of Pediatrics Sunderby Hospital Sunderby Sweden
| | | | - Eva Horemuzova
- Division of Pediatric Endocrinology Department of Women’s and Children’s Health Karolinska Institutet and University Hospital Stockholm Sweden
| | - Jovanna Dahlgren
- Göteborg Pediatric Growth Research Center Department of Pediatrics Institute of Clinical Sciences Sahlgrenska AcademyUniversity of Gothenburg Göteborg Sweden
| | - Magnus Burstedt
- Department of Medical Biosciences Medical and Clinical Genetics Umeå University Umeå Sweden
| | - Ola Nilsson
- Division of Pediatric Endocrinology Department of Women’s and Children’s Health Karolinska Institutet and University Hospital Stockholm Sweden
- Center for Molecular Medicine Karolinska Institutet and University Hospital Stockholm Sweden
- School of Medical Sciences Örebro University and University Hospital Örebro Sweden
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4
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Walenkamp MJE, Robers JML, Wit JM, Zandwijken GRJ, van Duyvenvoorde HA, Oostdijk W, Hokken-Koelega ACS, Kant SG, Losekoot M. Phenotypic Features and Response to GH Treatment of Patients With a Molecular Defect of the IGF-1 Receptor. J Clin Endocrinol Metab 2019; 104:3157-3171. [PMID: 30848790 DOI: 10.1210/jc.2018-02065] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 03/04/2019] [Indexed: 02/06/2023]
Abstract
CONTEXT The phenotype and response to GH treatment of children with an IGF1R defect is insufficiently known. OBJECTIVE To develop a clinical score for selecting children with short stature for genetic testing and evaluate the efficacy of treatment. DESIGN AND SETTING Case series with an IGF1R defect identified in a university genetic laboratory. PATIENTS AND INTERVENTIONS Of all patients with sufficient clinical data, 18 had (likely) pathogenic mutations (group 1) and 7 had 15q deletions including IGF1R (group 2); 19 patients were treated with GH. MAIN OUTCOME MEASURES Phenotype and response to GH treatment. RESULTS In groups 1 and 2, mean (range) birth weight, length, and head circumference (HC) SD scores (SDSs) were -2.1 (-3.7 to -0.4), -2.7 (-5.0 to -1.0), and -1.6 (-3.0 to 0.0), respectively. At presentation, height, HC, and serum IGF-1 SDSs were -3.0 (-5.5 to -1.7), -2.5 (-4.2 to -0.5), and +1.2 (-1.3 to 3.2), respectively. Feeding problems were reported in 15 of 19 patients. A clinical score with 76% sensitivity is proposed. After 3 years of GH treatment [1.1 (0.2) mg/m2/d] height gain in groups 1 (n = 12) and 2 (n = 7) was 0.9 SDS and 1.3 SDS (at a mean IGF-1 of 3.5 SDS), less than reported for small for gestational age (1.8 SDS). CONCLUSION A clinical score encompassing birth weight and/or length, short stature, microcephaly, and IGF-1 is useful for selecting patients for IGF1R analysis. Feeding problems are common and the growth response to GH treatment is moderate.
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Affiliation(s)
- Marie J E Walenkamp
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Jasmijn M L Robers
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Jan M Wit
- Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | | | | | - Wilma Oostdijk
- Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Anita C S Hokken-Koelega
- Dutch Growth Research Foundation, Rotterdam, Netherlands
- Department of Pediatrics, Subdivision of Endocrinology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Sarina G Kant
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Monique Losekoot
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
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5
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Andrade AC, Jee YH, Nilsson O. New Genetic Diagnoses of Short Stature Provide Insights into Local Regulation of Childhood Growth
. Horm Res Paediatr 2018; 88:22-37. [PMID: 28334714 DOI: 10.1159/000455850] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/03/2017] [Indexed: 12/12/2022] Open
Abstract
Idiopathic short stature is a common condition with a heterogeneous etiology. Advances in genetic methods, including genome sequencing techniques and bioinformatics approaches, have emerged as important tools to identify the genetic defects in families with monogenic short stature. These findings have contributed to the understanding of growth regulation and indicate that growth plate chondrogenesis, and therefore linear growth, is governed by a large number of genes important for different signaling pathways and cellular functions, including genetic defects in hormonal regulation, paracrine signaling, cartilage matrix, and fundamental cellular processes. In addition, mutations in the same gene can cause a wide phenotypic spectrum depending on the severity and mode of inheritance of the mutation.
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Affiliation(s)
- Anenisia C Andrade
- Division of Pediatric Endocrinology, Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Youn Hee Jee
- Section of Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Ola Nilsson
- Division of Pediatric Endocrinology, Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Medical Sciences, Örebro University and University Hospital, Örebro, Sweden
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Terry MB, Keegan THM, Houghton LC, Goldberg M, Andrulis IL, Daly MB, Buys SS, Wei Y, Whittemore AS, Protacio A, Bradbury AR, Chung WK, Knight JA, John EM. Pubertal development in girls by breast cancer family history: the LEGACY girls cohort. Breast Cancer Res 2017; 19:69. [PMID: 28595647 PMCID: PMC5465536 DOI: 10.1186/s13058-017-0849-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 05/03/2017] [Indexed: 01/29/2023] Open
Abstract
Background Pubertal milestones, such as onset of breast development and menstruation, play an important role in breast cancer etiology. It is unclear if these milestones are different in girls with a first- or second-degree breast cancer family history (BCFH). Methods In the LEGACY Girls Study (n = 1040), we examined whether three mother/guardian-reported pubertal milestones (having reached Tanner Stage 2 or higher (T2+) for breast and pubic hair development, and having started menstruation) differed by BCFH. We also examined whether associations between body size and race/ethnicity and pubertal milestones were modified by BCFH. We used mother/guardian reports as the primary measure of pubertal milestones, but also conducted sensitivity analyses using clinical Tanner measurements available for a subcohort (n = 204). We analyzed cross-sectional baseline data with logistic regression models for the entire cohort, and longitudinal data with Weibull survival models for the subcohort of girls that were aged 5–7 years at baseline (n = 258). Results BCFH was modestly, but not statistically significantly, associated with Breast T2+ (odds ratio (OR) = 1.36, 95% confidence interval (CI) = 0.88–2.10), with a stronger association seen in the subcohort of girls with clinical breast Tanner staging (OR = 2.20, 95% CI = 0.91–5.32). In a longitudinal analysis of girls who were aged 5–7 years at baseline, BCFH was associated with a 50% increased rate of having early breast development (hazard ratio (HR) = 1.49, 95% CI = 1.0–2.21). This association increased to twofold in girls who were not overweight at baseline (HR = 2.04, 95% CI = 1.29–3.21). BCFH was not associated with pubic hair development and post-menarche status. The median interval between onset of breast development and menarche was longer for BCFH+ than BCFH– girls (2.3 versus 1.7 years), suggesting a slower developmental tempo for BCFH+ girls. Associations between pubertal milestones and body size and race/ethnicity were similar in girls with or without a BCFH. For example, weight was positively associated with Breast T2+ in both girls with (OR = 1.06 per 1 kg, 95% CI = 1.03–1.10) and without (OR = 1.14 per 1 kg, 95% CI = 1.04–1.24) a BCFH. Conclusions These results suggest that BCFH may be related to earlier breast development and slower pubertal tempo independent of body size and race/ethnicity. Electronic supplementary material The online version of this article (doi:10.1186/s13058-017-0849-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mary Beth Terry
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA.
| | - Theresa H M Keegan
- Division of Hematology and Oncology, University of California (UC) Davis School of Medicine, and UC Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Lauren C Houghton
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Mandy Goldberg
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Irene L Andrulis
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Saundra S Buys
- Department of Medicine, University of Utah Health Sciences Center, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Ying Wei
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Alice S Whittemore
- Departments of Biomedical Data Sciences and Health Research and Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Angeline Protacio
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Angela R Bradbury
- Departments of Medicine, Hematology/Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Medical Ethics and Health Policy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wendy K Chung
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA.,Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Julia A Knight
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Esther M John
- Cancer Prevention Institute of California, Fremont, CA, USA.,Department of Health Research and Policy (Epidemiology), and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
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Abstract
Short stature is a common and heterogeneous condition that is often genetic in etiology. For most children with genetic short stature, the specific molecular causes remain unknown; but with advances in exome/genome sequencing and bioinformatics approaches, new genetic causes of growth disorders have been identified, contributing to the understanding of the underlying molecular mechanisms of longitudinal bone growth and growth failure. Identifying new genetic causes of growth disorders has the potential to improve diagnosis, prognostic accuracy, and individualized management, and help avoid unnecessary testing for endocrine and other disorders.
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Affiliation(s)
- Youn Hee Jee
- Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC, Room 1-3330, 10 Center Drive MSC 1103, Bethesda, MD 20892-1103, USA.
| | - Anenisia C Andrade
- Division of Pediatric Endocrinology, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Solnavägen 1, Solna 171 77, Sweden
| | - Jeffrey Baron
- Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC, Room 1-3330, 10 Center Drive MSC 1103, Bethesda, MD 20892-1103, USA
| | - Ola Nilsson
- Division of Pediatric Endocrinology, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Solnavägen 1, Solna 171 77, Sweden; University Hospital, Örebro University, Södra Grev Rosengatan, Örebro 701 85, Sweden
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8
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Harmel EM, Binder G, Barnikol-Oettler A, Caliebe J, Kiess W, Losekoot M, Ranke MB, Rappold GA, Schlicke M, Stobbe H, Wit JM, Pfäffle R, Klammt J. Alu-mediated recombination defect in IGF1R: haploinsufficiency in a patient with short stature. Horm Res Paediatr 2014; 80:431-42. [PMID: 24296753 DOI: 10.1159/000355410] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 08/05/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The insulin-like growth factor (IGF) receptor (IGF1R) is essential for normal development and growth. IGF1R mutations cause IGF-1 resistance resulting in intrauterine and postnatal growth failure. The phenotypic spectrum related to IGF1R mutations remains to be fully understood. METHODS Auxological and endocrinological data of a patient identified previously were assessed. The patient's fibroblasts were studied to characterize the IGF1R deletion, mRNA fate, protein expression and signalling capabilities. RESULTS The boy, who carries a heterozygous IGF1R exon 6 deletion caused by Alu element-mediated recombination and a heterozygous SHOX variant (p.Met240Ile), was born appropriate for gestational age but developed proportionate short stature postnatally. IGF-1 levels were low-normal. None of the stigmata associated with SHOX deficiency or sporadically observed in IGF1R mutation carriers were present. Nonsense-mediated mRNA decay led to a substantial decline of IGF1R dosage and IGF-1-dependent receptor autophosphorylation but not impaired downstream signalling. CONCLUSION We present the first detailed report of an intragenic IGF1R deletion identified in a patient who, apart from short stature, deviates from all established markers that qualify a growth-retarded child for IGF1R analysis. Although such children will usually escape routine clinical mutation screenings, they can contribute to the understanding of factors and mechanisms that cooperate with the IGF1R.
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Affiliation(s)
- Eva-Maria Harmel
- University Hospital for Children and Adolescents, Centre for Paediatric Research, Leipzig, Germany
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9
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Wang SR, Carmichael H, Andrew SF, Miller TC, Moon JE, Derr MA, Hwa V, Hirschhorn JN, Dauber A. Large-scale pooled next-generation sequencing of 1077 genes to identify genetic causes of short stature. J Clin Endocrinol Metab 2013; 98:E1428-37. [PMID: 23771920 PMCID: PMC3733853 DOI: 10.1210/jc.2013-1534] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
CONTEXT The majority of patients presenting with short stature do not receive a definitive diagnosis. Advances in genetic sequencing allow for large-scale screening of candidate genes, potentially leading to genetic diagnoses. OBJECTIVES The purpose of this study was to discover genetic variants that contribute to short stature in a cohort of children with no known genetic etiology. DESIGN This was a prospective cohort study of subjects with short stature. SETTING The setting was a pediatric endocrinology and genetics clinics at an academic center. PATIENTS A total of 192 children with short stature with no defined genetic etiology and 192 individuals of normal stature from the Framingham Heart Study were studied. INTERVENTION Pooled targeted sequencing using next-generation DNA sequencing technology of the exons of 1077 candidate genes was performed. MAIN OUTCOME MEASURES The numbers of rare nonsynonymous genetic variants found in case patients but not in control subjects, known pathogenic variants in case patients, and potentially pathogenic variants in IGF1R were determined. RESULTS We identified 4928 genetic variants in 1077 genes that were present in case patients but not in control subjects. Of those, 1349 variants were novel (898 nonsynonymous). False-positive rates from pooled sequencing were 4% to 5%, and the false-negative rate was 0.1% in regions covered well by sequencing. We identified 3 individuals with known pathogenic variants in PTPN11 causing undiagnosed Noonan syndrome. There were 9 rare potentially nonsynonymous variants in IGF1R, one of which is a novel, probably pathogenic, frameshift mutation. A previously reported pathogenic variant in IGF1R was present in a control subject. CONCLUSIONS Large-scale sequencing efforts have the potential to rapidly identify genetic etiologies of short stature, but data interpretation is complex. Noonan syndrome may be an underdiagnosed cause of short stature.
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Affiliation(s)
- Sophie R Wang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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