1
|
Gerrish A, Mashayamombe-Wolfgarten C, Stone E, Román-Montañana C, Abbott J, Jenkinson H, Millen G, Gurney S, McCalla M, Staveley SJ, Kainth A, Kirk M, Bowen C, Cavanagh S, Bunstone S, Carney M, Mohite A, Clokie S, Reddy MA, Foster A, Allen S, Parulekar M, Cole T. Genetic Diagnosis of Retinoblastoma Using Aqueous Humour-Findings from an Extended Cohort. Cancers (Basel) 2024; 16:1565. [PMID: 38672657 PMCID: PMC11049382 DOI: 10.3390/cancers16081565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/10/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
The identification of somatic RB1 variation is crucial to confirm the heritability of retinoblastoma. We and others have previously shown that, when tumour DNA is unavailable, cell-free DNA (cfDNA) derived from aqueous humour (AH) can be used to identify somatic RB1 pathogenic variation. Here we report RB1 pathogenic variant detection, as well as cfDNA concentration in an extended cohort of 75 AH samples from 68 patients. We show cfDNA concentration is highly variable and significantly correlated with the collection point of the AH. Cell-free DNA concentrations above 5 pg/µL enabled the detection of 93% of known or expected RB1 pathogenic variants. In AH samples collected during intravitreal chemotherapy treatment (Tx), the yield of cfDNA above 5 pg/µL and subsequent variant detection was low (≤46%). However, AH collected by an anterior chamber tap after one to three cycles of primary chemotherapy (Dx1+) enabled the detection of 75% of expected pathogenic variants. Further limiting our analysis to Dx1+ samples taken after ≤2 cycles (Dx ≤ 2) provided measurable levels of cfDNA in all cases, and a subsequent variant detection rate of 95%. Early AH sampling is therefore likely to be important in maximising cfDNA concentration and the subsequent detection of somatic RB1 pathogenic variants in retinoblastoma patients undergoing conservative treatment.
Collapse
Affiliation(s)
- Amy Gerrish
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
| | - Chipo Mashayamombe-Wolfgarten
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
| | - Edward Stone
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
- North West Genomic Laboratory Hub (Manchester), St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; (S.B.); (M.C.)
| | - Claudia Román-Montañana
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
| | - Joseph Abbott
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Helen Jenkinson
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Gerard Millen
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Sam Gurney
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Maureen McCalla
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Sarah-Jane Staveley
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Anu Kainth
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Maria Kirk
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Claire Bowen
- Birmingham Children’s Hospital Histopathology Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK (S.C.)
| | - Susan Cavanagh
- Birmingham Children’s Hospital Histopathology Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK (S.C.)
| | - Sancha Bunstone
- North West Genomic Laboratory Hub (Manchester), St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; (S.B.); (M.C.)
| | - Megan Carney
- North West Genomic Laboratory Hub (Manchester), St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; (S.B.); (M.C.)
| | - Ajay Mohite
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Samuel Clokie
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
| | - M. Ashwin Reddy
- Retinoblastoma Unit, Royal London Hospital, Barts Health NHS Trust, London E1 1BB, UK
| | - Alison Foster
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
| | - Stephanie Allen
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
| | - Manoj Parulekar
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
| |
Collapse
|
2
|
Ceroni F, Osborne D, Clokie S, Bax DA, Cassidy EJ, Dunn MJ, Harris CM, Self JE, Ragge NK. Analysis of Fibroblast Growth Factor 14 (FGF14) structural variants reveals the genetic basis of the early onset nystagmus locus NYS4 and variable ataxia. Eur J Hum Genet 2023; 31:353-359. [PMID: 36207621 PMCID: PMC9995494 DOI: 10.1038/s41431-022-01197-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/02/2022] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
Nystagmus (involuntary, rhythmical eye movements) can arise due to sensory eye defects, in association with neurological disorders or as an isolated condition. We identified a family with early onset nystagmus and additional neurological features carrying a partial duplication of FGF14, a gene associated with spinocerebellar ataxia type 27 (SCA27) and episodic ataxia. Detailed eye movement analysis revealed oculomotor anomalies strikingly similar to those reported in a previously described four-generation family with early onset nystagmus and linkage to a region on chromosome 13q31.3-q33.1 (NYS4). Since FGF14 lies within NYS4, we revisited the original pedigree using whole genome sequencing, identifying a 161 kb heterozygous deletion disrupting FGF14 and ITGBL1 in the affected individuals, suggesting an FGF14-related condition. Therefore, our study reveals the genetic variant underlying NYS4, expands the spectrum of pathogenic FGF14 variants, and highlights the importance of screening FGF14 in apparently isolated early onset nystagmus.
Collapse
Affiliation(s)
- Fabiola Ceroni
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Daniel Osborne
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Samuel Clokie
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Foundation Trust, Birmingham, UK
| | - Dorine A Bax
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Emma J Cassidy
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, UK
| | - Matt J Dunn
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK
| | | | - Jay E Self
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Nicola K Ragge
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK.
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Foundation Trust, Birmingham, UK.
| |
Collapse
|
3
|
Gerrish A, Bowns B, Mashayamombe-Wolfgarten C, Young E, Court S, Bott J, McCalla M, Ramsden S, Parks M, Goudie D, Carless S, Clokie S, Cole T, Allen S. Non-Invasive Prenatal Diagnosis of Retinoblastoma Inheritance by Combined Targeted Sequencing Strategies. J Clin Med 2020; 9:jcm9113517. [PMID: 33143217 PMCID: PMC7692133 DOI: 10.3390/jcm9113517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 12/24/2022] Open
Abstract
Retinoblastoma, the most common childhood eye cancer, presents in two forms: heritable or sporadic. Heritable retinoblastoma is caused by a germline mutation in the RB1 gene. Early diagnosis of children at risk of inheriting an RB1 mutation is crucial to achieve optimal clinical outcome. Currently, the majority of genetic testing is performed on newborns, which has multiple disadvantages for both families and the healthcare system. We have developed a non-invasive prenatal diagnosis (NIPD) service for retinoblastoma, available from 8 weeks’ gestation, which uses a combination of massively parallel sequencing (MPS) techniques, dependent on the inheritance model. Detection of paternal or suspected de novo RB1 variants is achieved through amplicon-based MPS. NIPD of a fetus at risk of maternal inheritance is performed using capture-based targeted sequencing and relative haplotype dosage analysis. In addition, we show proof of principle of how capture-based sequencing can be used for de novo variants unsuitable for amplicon-based testing. In total, we report the NIPD of 15 pregnancies, results of which show 100% concordance with all postnatal testing performed at the time of publication (n = 12) with remaining pregnancies ongoing. NIPD of retinoblastoma therefore offers a viable alternative to newborn genetic testing.
Collapse
Affiliation(s)
- Amy Gerrish
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
- Correspondence:
| | - Benjamin Bowns
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Chipo Mashayamombe-Wolfgarten
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Elizabeth Young
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Samantha Court
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Joshua Bott
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Maureen McCalla
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Simon Ramsden
- Manchester Centre For Genomic Medicine, University of Manchester, St Mary’s Hospital, Manchester Academic Health Science Centre, Manchester M13 9WL, UK;
| | - Michael Parks
- Nonacus Limted, Birmingham Research Park, Birmingham B15 2SQ, UK;
| | - David Goudie
- East of Scotland Regional Genetics Service, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK;
| | - Sue Carless
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Samuel Clokie
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Stephanie Allen
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| |
Collapse
|
4
|
Young E, Bowns B, Gerrish A, Parks M, Court S, Clokie S, Mashayamombe-Wolfgarten C, Hewitt J, Williams D, Cole T, Allen S. Clinical Service Delivery of Noninvasive Prenatal Diagnosis by Relative Haplotype Dosage for Single-Gene Disorders. J Mol Diagn 2020; 22:1151-1161. [PMID: 32553884 PMCID: PMC7471768 DOI: 10.1016/j.jmoldx.2020.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/30/2020] [Accepted: 06/01/2020] [Indexed: 11/17/2022] Open
Abstract
A relative haplotype dosage (RHDO)-based method was developed and implemented into routine clinical practice for noninvasive prenatal diagnosis (NIPD) of multiple single-gene disorders: spinal muscular atrophy, Duchenne and Becker muscular dystrophies, and cystic fibrosis. This article describes the experiences of the first 152 pregnancies to have NIPD by RHDO as part of a routine clinical service. Provision of results within a clinically useful time frame (mean, 11 calendar days) was shown to be possible, with a very low failure rate (4%), none being due to a technical failure. Where follow-up confirmatory testing was performed for audit purposes, 100% concordance was seen with the NIPD result, and no discrepancies have been reported. The robust performance of the assay, together with high sensitivity and specificity, demonstrates that NIPD by RHDO is feasible for use in a clinical setting.
Collapse
Affiliation(s)
- Elizabeth Young
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, United Kingdom.
| | - Benjamin Bowns
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, United Kingdom
| | - Amy Gerrish
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, United Kingdom
| | - Michael Parks
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, United Kingdom
| | - Samantha Court
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, United Kingdom
| | - Samuel Clokie
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, United Kingdom
| | - Chipo Mashayamombe-Wolfgarten
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, United Kingdom
| | - Julie Hewitt
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, United Kingdom
| | - Denise Williams
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, United Kingdom
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, United Kingdom
| | - Stephanie Allen
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, United Kingdom
| |
Collapse
|
5
|
Gerrish A, Stone E, Clokie S, Ainsworth JR, Jenkinson H, McCalla M, Hitchcott C, Colmenero I, Allen S, Parulekar M, Cole T. Non-invasive diagnosis of retinoblastoma using cell-free DNA from aqueous humour. Br J Ophthalmol 2019; 103:bjophthalmol-2018-313005. [PMID: 30745306 PMCID: PMC6709774 DOI: 10.1136/bjophthalmol-2018-313005] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/19/2018] [Accepted: 12/22/2018] [Indexed: 11/03/2022]
Abstract
Retinoblastoma is the most common eye malignancy in childhood caused by mutations in the RB1 gene. Both alleles of the RB1 gene must be mutated for tumour development. The initial RB1 mutation may be constitutional germline or somatic (originating in one retinal cell only). Distinguishing between these alternative mechanisms is crucial, with wider implications for management of the patient and family members. Bilateral retinoblastoma is nearly always due to a constitutional mutation; however, approximately 15% of unilateral cases also carry a germline mutation, and identifying these cases is important. This can be achieved by identifying both mutation types in tumour tissue and excluding their presence in blood. Modern eye-saving chemotherapy treatment (systemic, intra-arterial and intravitreal) has resulted in fewer enucleations. As a result, tumour tissue required to identify sporadic RB1 mutation(s) is not always available. Modern intravitreal chemotherapeutic techniques for retinoblastoma involve aspiration of aqueous humour (AH), providing a novel sample source for analysis. By analysing cell-free DNA present in the AH fluid of eyes affected with retinoblastoma, we have developed a screening test capable of detecting somatic RB1 mutations that is comparable to current tests on enucleated tumour tissue. The results obtained with fluid from enucleated eyes were concordant with tumour tissue in all 10 cases analysed. In addition, AH analysis from two patients undergoing intravitreal chemotherapy successfully identified somatic variants in both cases. Our findings suggest that AH fluid is a promising source of tumour-derived DNA in retinoblastoma for analysis.
Collapse
Affiliation(s)
- Amy Gerrish
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Edward Stone
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Samuel Clokie
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - John R Ainsworth
- Birmingham Children's Hospital Eye Department, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Helen Jenkinson
- Birmingham Children's Hospital Eye Department, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Maureen McCalla
- Birmingham Children's Hospital Eye Department, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Carol Hitchcott
- Birmingham Children's Hospital Eye Department, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Isabel Colmenero
- Department of Histopathology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Stephanie Allen
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Manoj Parulekar
- Birmingham Children's Hospital Eye Department, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| |
Collapse
|
6
|
Hughes LA, McKay-Bounford K, Webb EA, Dasani P, Clokie S, Chandran H, McCarthy L, Mohamed Z, Kirk JMW, Krone NP, Allen S, Cole TRP. Next generation sequencing (NGS) to improve the diagnosis and management of patients with disorders of sex development (DSD). Endocr Connect 2019; 8:100-110. [PMID: 30668521 PMCID: PMC6373624 DOI: 10.1530/ec-18-0376] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 01/16/2019] [Indexed: 11/08/2022]
Abstract
Disorders of sex development (DSDs) are a diverse group of conditions where the chromosomal, gonadal or anatomical sex can be atypical. The highly heterogeneous nature of this group of conditions often makes determining a genetic diagnosis challenging. Prior to next generation sequencing (NGS) technologies, genetic diagnostic tests were only available for a few of the many DSD-associated genes, which consequently had to be tested sequentially. Genetic testing is key in establishing the diagnosis, allowing for personalised management of these patients. Pinpointing the molecular cause of a patient's DSD can significantly impact patient management by informing future development needs, altering management strategies and identifying correct inheritance pattern when counselling family members. We have developed a 30-gene NGS panel, designed to be used as a frontline test for all suspected cases of DSD (both 46,XX and 46,XY cases). We have confirmed a diagnosis in 25 of the 80 patients tested to date. Confirmed diagnoses were linked to mutations in AMH, AMHR2, AR, HSD17B3, HSD3B2, MAMLD1, NR5A1, SRD5A2 and WT1 which have resulted in changes to patient management. The minimum diagnostic yield for patients with 46,XY DSD is 25/73. In 34/80 patients, only benign or likely benign variants were identified, and in 21/80 patients only variants of uncertain significance (VOUS) were identified, resulting in a diagnosis not being confirmed in these individuals. Our data support previous studies that an NGS panel approach is a clinically useful and cost-effective frontline test for patients with DSDs.
Collapse
Affiliation(s)
- L A Hughes
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - K McKay-Bounford
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - E A Webb
- Department of Endocrinology & Diabetes, Birmingham Women’s and Children’s Hospital, Birmingham, UK
| | - P Dasani
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - S Clokie
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - H Chandran
- Department of Endocrinology & Diabetes, Birmingham Women’s and Children’s Hospital, Birmingham, UK
| | - L McCarthy
- Department of Endocrinology & Diabetes, Birmingham Women’s and Children’s Hospital, Birmingham, UK
| | - Z Mohamed
- Department of Endocrinology & Diabetes, Birmingham Women’s and Children’s Hospital, Birmingham, UK
| | - J M W Kirk
- Department of Endocrinology & Diabetes, Birmingham Women’s and Children’s Hospital, Birmingham, UK
| | - N P Krone
- Department of Endocrinology & Diabetes, Birmingham Women’s and Children’s Hospital, Birmingham, UK
| | - S Allen
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - T R P Cole
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
- Correspondence should be addressed to T R P Cole:
| |
Collapse
|
7
|
Watson LM, Bamber E, Schnekenberg RP, Williams J, Bettencourt C, Lickiss J, Jayawant S, Fawcett K, Clokie S, Wallis Y, Clouston P, Sims D, Houlden H, Becker EB, Németh AH. Dominant Mutations in GRM1 Cause Spinocerebellar Ataxia Type 44. Am J Hum Genet 2017; 101:866. [PMID: 29100096 PMCID: PMC5673670 DOI: 10.1016/j.ajhg.2017.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
8
|
Watson CM, Camm N, Crinnion LA, Clokie S, Robinson RL, Adlard J, Charlton R, Markham AF, Carr IM, Bonthron DT. Increased Sensitivity of Diagnostic Mutation Detection by Re-analysis Incorporating Local Reassembly of Sequence Reads. Mol Diagn Ther 2017; 21:685-692. [DOI: 10.1007/s40291-017-0304-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
9
|
Watson LM, Bamber E, Schnekenberg RP, Williams J, Bettencourt C, Jayawant S, Lickiss J, Fawcett K, Clokie S, Wallis Y, Clouston P, Sims D, Houlden H, Becker EB, Németh AH. Dominant Mutations in GRM1 Cause Spinocerebellar Ataxia Type 44. Am J Hum Genet 2017; 101:638. [PMID: 28985497 PMCID: PMC5630189 DOI: 10.1016/j.ajhg.2017.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
10
|
Watson LM, Bamber E, Schnekenberg RP, Williams J, Bettencourt C, Lickiss J, Jayawant S, Fawcett K, Clokie S, Wallis Y, Clouston P, Sims D, Houlden H, Becker EB, Németh AH. Dominant Mutations in GRM1 Cause Spinocerebellar Ataxia Type 44. Am J Hum Genet 2017; 101:451-458. [PMID: 28886343 PMCID: PMC5591020 DOI: 10.1016/j.ajhg.2017.08.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 07/25/2017] [Indexed: 12/15/2022] Open
Abstract
The metabotropic glutamate receptor 1 (mGluR1) is abundantly expressed in the mammalian central nervous system, where it regulates intracellular calcium homeostasis in response to excitatory signaling. Here, we describe heterozygous dominant mutations in GRM1, which encodes mGluR1, that are associated with distinct disease phenotypes: gain-of-function missense mutations, linked in two different families to adult-onset cerebellar ataxia, and a de novo truncation mutation resulting in a dominant-negative effect that is associated with juvenile-onset ataxia and intellectual disability. Crucially, the gain-of-function mutations could be pharmacologically modulated in vitro using an existing FDA-approved drug, Nitazoxanide, suggesting a possible avenue for treatment, which is currently unavailable for ataxias.
Collapse
|
11
|
Parks M, Court S, Bowns B, Cleary S, Clokie S, Hewitt J, Williams D, Cole T, MacDonald F, Griffiths M, Allen S. Non-invasive prenatal diagnosis of spinal muscular atrophy by relative haplotype dosage. Eur J Hum Genet 2017; 25:416-422. [PMID: 28120840 PMCID: PMC5386415 DOI: 10.1038/ejhg.2016.195] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 11/02/2016] [Accepted: 11/22/2016] [Indexed: 11/10/2022] Open
Abstract
Although technically possible, few clinical laboratories across the world have implemented non-invasive prenatal diagnosis (NIPD) for selected single-gene disorders, mostly owing to the elevated costs incurred. Having previously proven that NIPD for X-linked disorders can be feasibly implemented in clinical practice, we have now developed a test for the NIPD of an autosomal-recessive disorder, spinal muscular atrophy (SMA). Cell-free DNA was extracted from maternal blood and prepared for massively parallel sequencing on an Illumina MiSeq by targeted capture enrichment of single-nucleotide polymorphisms across a 6 Mb genomic window on chromosome 5 containing the SMN1 gene. Maternal, paternal and proband DNA samples were also tested for haplotyping purposes. Sequencing data was analysed by relative haplotype dosage (RHDO). Six pregnant SMA carriers and 10 healthy pregnant donors were recruited through the NIPSIGEN study. Inheritance of the maternally and paternally derived alleles of the affected SMN1 gene was determined in the foetus by RHDO analysis for autosomal-recessive disorders. DNA from the proband (for SMA carriers) or an invasively obtained foetal sample (for healthy pregnant donors) was used to identify the maternal and paternal reference haplotypes associated with the affected SMN1 gene. Results for all patients correlated with known outcomes and showed a testing specificity and sensitivity of 100%. On top of showing high accuracy and reliability throughout the stages of validation, our novel test for NIPD of SMA is also affordable and viable for implementation into clinical service.
Collapse
Affiliation(s)
- Michael Parks
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Samantha Court
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Benjamin Bowns
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Siobhan Cleary
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Samuel Clokie
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Julie Hewitt
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Denise Williams
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Fiona MacDonald
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Mike Griffiths
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| |
Collapse
|
12
|
Parks M, Court S, Cleary S, Clokie S, Hewitt J, Williams D, Cole T, MacDonald F, Griffiths M, Allen S. Non-invasive prenatal diagnosis of Duchenne and Becker muscular dystrophies by relative haplotype dosage. Prenat Diagn 2016; 36:312-20. [PMID: 26824862 PMCID: PMC4864947 DOI: 10.1002/pd.4781] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/25/2016] [Accepted: 01/26/2016] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Development of an accurate and affordable test for the non-invasive prenatal diagnosis of Duchenne and Becker muscular dystrophies (DMD/BMD) to implement in clinical practice. METHOD Cell-free DNA was extracted from maternal blood and prepared for massively parallel sequencing on an Illumina MiSeq by targeted capture enrichment of single nucleotide polymorphisms (SNPs) across the dystrophin gene on chromosome X. Sequencing data were analysed by relative haplotype dosage. RESULTS Seven healthy pregnant donors and two pregnant DMD carriers all bearing a male fetus were recruited through the non-invasive prenatal diagnosis for single gene disorders study. Non-invasive prenatal diagnosis testing was conducted by relative haplotype dosage analysis for X-linked disorders where the genomic DNA from the chorionic villus sampling (for healthy pregnant donors) or from the proband (for pregnant DMD carriers) was used to identify the reference haplotype. Results for all patients showed a test accuracy of 100%, when the calculated fetal fraction was >4% and correlated with known outcomes. A recombination event was also detected in a DMD patient. CONCLUSION Our new test for NIPD of DMD/BMD has been shown to be accurate and reliable during initial stages of validation. It is also feasible for implementation into clinical service.
Collapse
Affiliation(s)
- Michael Parks
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Samantha Court
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Siobhan Cleary
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Samuel Clokie
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Julie Hewitt
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Denise Williams
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Trevor Cole
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Fiona MacDonald
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Mike Griffiths
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| |
Collapse
|
13
|
Abstract
Cone-rod homeobox (Crx) encodes Crx, a transcription factor expressed selectively in retinal photoreceptors and pinealocytes, the major cell type of the pineal gland. In this study, the influence of Crx on the mammalian pineal gland was studied by light and electron microscopy and by use of microarray and qRTPCR technology, thereby extending previous studies on selected genes (Furukawa et al. 1999). Deletion of Crx was not found to alter pineal morphology, but was found to broadly modulate the mouse pineal transcriptome, characterized by a>2-fold down-regulation of 543 genes and a>2-fold up-regulation of 745 genes (p<0.05). Of these, one of the most highly up-regulated (18-fold) was Hoxc4, a member of the Hox gene family, members of which are known to control gene expression cascades. During a 24-h period, a set of 51 genes exhibited differential day/night expression in pineal glands of wild-type animals; only eight of these were also day/night expressed in the Crx⁻/⁻ pineal gland. However, in the Crx⁻/⁻ pineal gland 41 genes exhibited differential night/day expression that was not seen in wild-type animals. These findings indicate that Crx broadly modulates the pineal transcriptome and also influences differential night/day gene expression in this tissue. Some effects of Crx deletion on the pineal transcriptome might be mediated by Hoxc4 up-regulation.
Collapse
Affiliation(s)
- Louise Rovsing
- Department of Neuroscience and Pharmacology, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Abstract
We have previously shown that casein kinase (CK) Ialpha from mammalian brain phosphorylates 14-3-3 zeta and tau isoforms on residue 233. In the present study, we show that CKIalpha associates with 14-3-3 both in vitro and in vivo. The interaction between CKIalpha and 14-3-3 is dependent on CKIalpha phosphorylation, unlike centaurin-alpha1 (also known as ADAP1), which binds to unphosphorylated CKIalpha on the same region. CKIalpha preferentially interacts with mammalian eta and gamma 14-3-3 isoforms, and peptides that bind to the 14-3-3 binding pocket prevent this interaction. The region containing Ser218 in this CKIalpha binding site was mutated and the interaction between CKIalpha and 14-3-3 was reduced. We subsequently identified a second phosphorylation-dependent 14-3-3 binding site within CKIalpha containing Ser242 that may be the principal site of interaction. We also show that both fission and budding yeast CKI kinase homologues phosphorylate mammalian and budding yeast (BMH1 and BMH2) 14-3-3 at the equivalent site.
Collapse
Affiliation(s)
- Samuel Clokie
- Institute of Structural Biology, Edinburgh University, UK
| | | | | | | | | |
Collapse
|
15
|
Aitken A, Baxter H, Dubois T, Clokie S, Mackie S, Mitchell K, Peden A, Zemlickova E. Specificity of 14-3-3 isoform dimer interactions and phosphorylation. Biochem Soc Trans 2002; 30:351-60. [PMID: 12196094 DOI: 10.1042/bst0300351] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Proteins that interact with 14-3-3 isoforms are involved in regulation of the cell cycle, intracellular trafficking/targeting, signal transduction, cytoskeletal structure and transcription. Recent novel roles for 14-3-3 isoforms include nuclear trafficking the direct interaction with cruciform DNA and with a number of receptors, small G-proteins and their regulators. Recent findings also show that the mechanism of interaction is also more complex than the initial finding of the novel phosphoserine/threonine motif. Non-phosphorylated binding motifs that can also be of high affinity may show a more isoform-dependent interaction and binding of a protein through two distinct binding motifs to a dimeric 14-3-3 may also be essential for full interaction. Phosphorylation of specific 14-3-3 isoforms can also regulate interactions. In many cases, they show a distinct preference for a particular isoform(s) of 14-3-3. A specific repertoire of dimer formation may influence which of the 14-3-3-interacting proteins could be brought together. Mammalian and yeast 14-3-3 isoforms show a preference for dimerization with specific partners in vivo.
Collapse
Affiliation(s)
- A Aitken
- University of Edinburgh, Division of Biomedical and Clinical Laboratory Sciences, Hugh Robson Building, George Square, Edinburgh EH8 9XD, Scotland, UK.
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Baxter HC, Fraser JR, Liu WG, Forster JL, Clokie S, Steinacker P, Otto M, Bahn E, Wiltfang J, Aitken A. Specific 14-3-3 isoform detection and immunolocalization in prion diseases. Biochem Soc Trans 2002; 30:387-91. [PMID: 12196100 DOI: 10.1042/bst0300387] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
14-3-3 proteins are involved in signalling processes in neuronal cells. Using isoform-specific antibodies we have examined the variation in 14-3-3 isoform neurolocation in normal and scrapie-infected murine brain and show that in defined areas of the brain there are significant changes associated with the pathology of the disease process. The appearance of 14-3-3 proteins in the cerebrospinal fluid (CSF) is a consequence of neuronal disease and the detection of specific isoforms of the 14-3-3 proteins in the CSF is characteristic of some neurodegenerative diseases. In this study, monitoring specifically for the gamma 14-3-3 isoform in the CSF by both Western-blot analysis and ELISA we can show a level of correlation between the assays.
Collapse
Affiliation(s)
- H C Baxter
- Department of Biomedical Sciences, University of Edinburgh, George Square, Edinburgh EH8 9XD, UK.
| | | | | | | | | | | | | | | | | | | |
Collapse
|