1
|
Sicko RJ, Romitti PA, Browne ML, Brody LC, Stevens CF, Mills JL, Caggana M, Kay DM. Rare Variants in RPPH1 Real-Time Quantitative PCR Control Assay Binding Sites Result in Incorrect Copy Number Calls. J Mol Diagn 2022; 24:33-40. [PMID: 34656763 PMCID: PMC8802765 DOI: 10.1016/j.jmoldx.2021.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/21/2021] [Accepted: 09/15/2021] [Indexed: 01/03/2023] Open
Abstract
Real-time quantitative PCR (qPCR) using RPPH1 as a reference gene is a standard method for assessment and validation of genomic copy number variations. However, variants in the reference amplicon may cause errors, which was investigated herein. While conducting copy number variation validations for birth defects research studies, 13 of 1634 specimens with multiple loci that appeared to be present as three copies were unexpectedly detected. This apparent trisomy was hypothesized to be an amplification artifact caused by a variant in the RPPH1 amplicon. Sequencing revealed all 13 individuals carried one of the four different variants within the RPPH1 amplicon. These variants could produce allelic dropout or altered reaction efficiency, causing an inaccurate measurement of copy number. Additional genotyping predicted a low frequency of the most common variant (rs3093876; 14/3562 alleles; minor allele frequency, 0.39%). Laboratories should recognize the potential for inaccurate results when using a single qPCR control assay. Overestimated CFTR and SMN2 copy numbers identified during newborn screening that otherwise would have been incorrectly called were also detected. Variants in reference loci may produce false-negative normal results for test loci when real deletions are present. For clinical laboratories screening for heterozygous deletions for diagnostic testing or prenatal/carrier screening via qPCR, the most cost-effective solution to maximize sensitivity is to run triplex reactions targeting the region of interest with two control genes.
Collapse
Affiliation(s)
- Robert J Sicko
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, Iowa
| | - Marilyn L Browne
- Birth Defects Registry, New York State Department of Health, Albany, New York; University at Albany School of Public Health, Rensselaer, New York
| | - Lawrence C Brody
- Genetics and Environment Interaction Section, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Colleen F Stevens
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - James L Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland
| | - Michele Caggana
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Denise M Kay
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York.
| |
Collapse
|
2
|
Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn Screening. Int J Neonatal Screen 2021; 7:ijns7040073. [PMID: 34842611 PMCID: PMC8628990 DOI: 10.3390/ijns7040073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Newborn screening (NBS) for Cystic Fibrosis (CF) is associated with improved outcomes. All US states screen for CF; however, CF NBS algorithms have high false positive (FP) rates. In New York State (NYS), the positive predictive value of CF NBS improved from 3.7% to 25.2% following the implementation of a three-tier IRT-DNA-SEQ approach using commercially available tests. Here we describe a modification of the NYS CF NBS algorithm via transition to a new custom next-generation sequencing (NGS) platform for more comprehensive cystic fibrosis transmembrane conductance regulator (CFTR) gene analysis. After full gene sequencing, a tiered strategy is used to first analyze only a specific panel of 338 clinically relevant CFTR variants (second-tier), followed by unblinding of all sequence variants and bioinformatic assessment of deletions/duplications in a subset of samples requiring third-tier analysis. We demonstrate the analytical and clinical validity of the assay and the feasibility of use in the NBS setting. The custom assay has streamlined our molecular workflow, increased throughput, and allows for bioinformatic customization of second-tier variant panel content. NBS aims to identify those infants with the highest disease risk. Technological molecular improvements can be applied to NBS algorithms to reduce the burden of FP referrals without loss of sensitivity.
Collapse
|
3
|
Niemyjski EA, Ischander M. EX18_21 large duplication: A novel pathogenic mutation of the CFTR gene for cystic fibrosis. Pediatr Pulmonol 2021; 56:11-13. [PMID: 33118704 DOI: 10.1002/ppul.25118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/01/2020] [Accepted: 10/03/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Emily A Niemyjski
- Department of Pediatrics, Section of Neonatology, Baylor College of Medicine, Houston, Texas, USA
| | - Mariam Ischander
- Department of Pediatric and Adolescent Medicine, Division of Pediatric Pulmonology, Western Michigan University, Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, USA
| |
Collapse
|
4
|
Petrova NV, Kashirskaya NY, Vasilyeva TA, Kondratyeva EI, Zhekaite EK, Voronkova AY, Sherman VD, Galkina VA, Ginter EK, Kutsev SI, Marakhonov AV, Zinchenko RA. Analysis of CFTR Mutation Spectrum in Ethnic Russian Cystic Fibrosis Patients. Genes (Basel) 2020; 11:E554. [PMID: 32429104 PMCID: PMC7288340 DOI: 10.3390/genes11050554] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/08/2020] [Accepted: 05/13/2020] [Indexed: 12/14/2022] Open
Abstract
The distribution and frequency of the CFTR gene mutations vary considerably between countries and ethnic groups. Russians are an East Slavic ethnic groups are native to Eastern Europe. Russians, the most numerous people of the Russian Federation (RF), make about 80% of the population. The aim is to reveal the molecular causes of CF in ethnic Russian patients as comprehensively as possible. The analysis of most common CFTR mutations utilized for CF diagnosis in multiethnic RF population accounts for about 83% of all CF-causing mutations in 1384 ethnic Russian patients. Variants c.1521_1523delCTT (F508del), c.54-5940_273+10250del21kb (CFTRdele2,3), c.2012delT (2143delT), c.2052_2053insA (2184insA), and c.3691delT (3821delT) are most typical for CF patients of Russian origin. DNA of 154 CF patients, Russian by origin, in whom at least one mutant allele was not previously identified (164 CF alleles), was analyzed by Sanger sequencing followed by the multiplex ligase-dependent probe amplification (MLPA) method. In addition to the 29 variants identified during the previous test for common mutations, 91 pathogenic CFTR variants were also revealed: 29 missense, 19 nonsense, 14 frame shift in/del, 17 splicing, 1 in frame ins, and 11 copy number variations (CNV). Each of the 61 variants was revealed once, and 17 twice. Each of the variants c.1209G>C (E403D), c.2128A>T (K710X), c.3883delA (4015delA), and c.3884_3885insT (4016insT) were detected for three, c.1766+1G>A (1898+1G>A) and c.2834C>T (S945L) for four, c.1766+1G>C (1898+1G>C) and c.(743+1_744-1)_(1584+1_1585-1)dup (CFTRdup6b-10) for five, c.2353C>T (R785X) and c.4004T>C (L1335P) for six, c.3929G>A (W1310X) for seven, c.580-1G>T (712-1G>T for eight, and c.1240_1244delCAAAA (1365del5) for 11 unrelated patients. A comprehensive analysis of CFTR mutant alleles with sequencing followed by MLPA, allowed not only the identification of 163 of 164 unknown alleles in our patient sample, but also expansion of the mutation spectrum with novel and additional frequent variants for ethnic Russians.
Collapse
Affiliation(s)
- Nika V. Petrova
- Research Centre for Medical Genetics, Moskvorechje Street, 1, 115478 Moscow, Russia; (N.Y.K.); (T.A.V.); (E.I.K.); (E.K.Z.); (A.Y.V.); (V.D.S.); (V.A.G.); (E.K.G.); (S.I.K.); (A.V.M.); (R.A.Z.)
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Petrova NV, Marakhonov AV, Vasilyeva TA, Kashirskaya NY, Ginter EK, Kutsev SI, Zinchenko RA. Comprehensive genotyping reveals novel CFTR variants in cystic fibrosis patients from the Russian Federation. Clin Genet 2018; 95:444-447. [PMID: 30548586 DOI: 10.1111/cge.13477] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 11/28/2022]
Abstract
Single nucleotide variants are represented as lines. The height of the line corresponds to the allele frequency. Gross chromosomal copy number variations are shown as arrows. Color corresponds to the mutation type. Complex alleles represented with a clip. Previously reported variants are located above the schematic gene representation. Their names are presented in Table 1 in main text. Novel variants are depicted beneath the schematic gene representation.
Collapse
Affiliation(s)
- Nika V Petrova
- Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics (RCMG), Moscow, Russia
| | - Andrey V Marakhonov
- Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics (RCMG), Moscow, Russia
| | - Tatiana A Vasilyeva
- Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics (RCMG), Moscow, Russia
| | - Natalya Y Kashirskaya
- Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics (RCMG), Moscow, Russia
| | - Evgeny K Ginter
- Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics (RCMG), Moscow, Russia
| | - Sergey I Kutsev
- Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics (RCMG), Moscow, Russia.,Chair of Molecular and Cellular Genetics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Rena A Zinchenko
- Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics (RCMG), Moscow, Russia.,Chair of Molecular and Cellular Genetics, Pirogov Russian National Research Medical University, Moscow, Russia
| |
Collapse
|
6
|
Adyan TA, Stepanova AA, Krasovskiy SA, Polyakov AV. Updating Diagnostic Spectrum of Recurring CFTR Mutations. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418100022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
7
|
Celestino-Soper PBS, Simpson E, Tumbleson Brink D, Lynnes TC, Dlouhy S, Vatta M, Yeley J, Brown C, Bai S. Intragenic CFTR Duplication and 5T/12TG Variant in a Patient with Non-Classic Cystic Fibrosis. Sci Rep 2016; 6:38776. [PMID: 27996019 PMCID: PMC5172161 DOI: 10.1038/srep38776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 11/10/2016] [Indexed: 11/09/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disorder characterized by the accumulation of sticky and heavy mucus that can damage several organs. CF shows variable expressivity in affected individuals, but it typically causes respiratory and digestive complications as well as congenital bilateral absence of the vas deferens in males. Individuals with classic CF usually have variants that produce a defective protein from both alleles of the CFTR gene. Individuals with other variants may present with classic, non-classic, or milder forms of CF due to lower levels of functional CFTR protein. This article reports the genetic analysis of a female with features of asthma and mild or non-classic CF. CFTR sequencing demonstrated that she is a carrier for a maternally derived 5T/12TG variant. Deletion/duplication analysis by multiplex ligation-dependent probe amplification (MLPA) showed the presence of an intragenic paternally derived duplication involving exons 7-11 of the CFTR gene. This duplication is predicted to result in the production of a truncated CFTR protein lacking the terminal part of the nucleotide-binding domain 1 (NBD1) and thus is likely to be a non-functioning allele. The combination of this large intragenic duplication and 5T/12TG is the probable cause of the mild or non-classic CF features in this individual.
Collapse
Affiliation(s)
| | - Edward Simpson
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Danika Tumbleson Brink
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Ty C. Lynnes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Stephen Dlouhy
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Matteo Vatta
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Krannert Institute of Cardiology, Division of Cardiology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jana Yeley
- Division of Pulmonary, Allergy, Critical Care, Occupational, and Sleep Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Cynthia Brown
- Division of Pulmonary, Allergy, Critical Care, Occupational, and Sleep Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Shaochun Bai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| |
Collapse
|
8
|
A wide methodological approach to identify a large duplication in CFTR gene in a CF patient uncharacterised by sequencing analysis. J Cyst Fibros 2012; 10:412-7. [PMID: 21852204 DOI: 10.1016/j.jcf.2011.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 06/17/2011] [Accepted: 06/18/2011] [Indexed: 02/03/2023]
Abstract
BACKGROUND PCR-based diagnostic procedures are not able to characterise 6% of CF alleles. Recently, the application of array-CGH and of CFTR mRNA analysis has allowed the identification of new copy number mutations and splicing defects, that account for 2% and 13% of CF alleles, respectively, in the Italian population. METHODS Here, we report the characterisation of a large duplication in CFTR gene through different methods: MLPA assay, RT-PCR and high-resolution array-CGH. RESULTS We identified a large duplication, involving exons 6b-16, in a patient heterozygous for F508del mutation. This duplication produces an abnormal transcript with an out of frame addition of 2244 nucleotides and leads to the insertion of 8 amino-acid residues in the protein, followed by a stop codon. CONCLUSIONS We propose a wide methodological approach based on MLPA assay, RT-PCR and high-resolution array-CGH to routinely analyse CF patients uncharacterised for one or both CFTR alleles.
Collapse
|
9
|
Hantash FM, Rebuyon A, Peng M, Redman JB, Sun W, Strom CM. Apparent homozygosity of a novel frame shift mutation in the CFTR gene because of a large deletion. J Mol Diagn 2009; 11:253-6. [PMID: 19324987 DOI: 10.2353/jmoldx.2009.080117] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Patients develop cystic fibrosis because of a variety of homozygous recessive mutations, including single nucleotide polymorphisms, insertions, and deletions, in the cystic fibrosis transmembrane regulator (CFTR) gene, or because of compound heterozygosity for two mutations in the CFTR gene. A false determination of homozygosity for a particular CFTR mutation could negatively affect both carrier screens for a patient's family as well as researchers' ability to study the physiological implications of a particular mutation. We argued previously that homozygosity for rare or novel mutations in the CFTR gene could result from a mutation on one allele and the presence of a large deletion encompassing the same sequence region on the second allele. We present here a patient with classic cystic fibrosis who has a novel microdeletion in exon 7 on one allele and a large deletion encompassing exon 7 on the second allele. These data highlight the need to prevent misdiagnosis of homozygous mutations, which can lead to misinterpretation of mutation penetrance and its effects on protein function.
Collapse
Affiliation(s)
- Feras M Hantash
- Department of Molecular Genetics, Quest Diagnostics Nichols Institute, San Juan Capistrano, California 92690, USA.
| | | | | | | | | | | |
Collapse
|
10
|
Schrijver I, Rappahahn K, Pique L, Kharrazi M, Wong LJ. Multiplex ligation-dependent probe amplification identification of whole exon and single nucleotide deletions in the CFTR gene of Hispanic individuals with cystic fibrosis. J Mol Diagn 2008; 10:368-75. [PMID: 18556774 DOI: 10.2353/jmoldx.2008.080004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A disparity between Caucasian and Hispanic mutation detection for cystic fibrosis continues to exist, although the carrier frequency is only moderately lower in Hispanics. We aimed to identify exonic rearrangements that remained undetected by conventional methods. In seven of 32 cystic fibrosis-affected self-identified Hispanics for whom only one or no mutations were identified by extensive molecular testing, exon deletions appeared to be present with a multiplex ligation-dependent probe amplification (MLPA) assay. Two recurrent deletions (of exons 2-3 and exons 22-23) were identified in one and three patients, respectively (12.5%, 11.1% of unidentified alleles). Two apparently novel deletions (exons 6b and 20) were identified in three additional patients. Subsequent sequencing to characterize deletion breakpoints, however, identified single nucleotide deletions at the probe binding sites close to the ligation point. All resulted in false positive MLPA deletion signals. Interestingly, these mutations were not common in Caucasians, and one (935delA) was common in U.S. Hispanics. On examination of all probe binding sites, we identified a total of 76 reported mutations and five silent variants that immediately surrounded the MLPA ligation sites, with 22 occurring in non-Caucasians. These mutations are not all rare. Thus, apparent exon deletions by MLPA may indicate the presence of both large deletions and point mutations, with important implications for pan-ethnic MLPA testing in cystic fibrosis and other genetic conditions.
Collapse
Affiliation(s)
- Iris Schrijver
- Department of Pathology L235, Stanford University Medical Center, 300 Pasteur Drive, Stanford, CA 94305, USA.
| | | | | | | | | |
Collapse
|
11
|
Chou LS, Lyon E, Mao R. Molecular diagnosis utility of multiplex ligation-dependent probe amplification. ACTA ACUST UNITED AC 2008; 2:373-85. [DOI: 10.1517/17530059.2.4.373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|