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Nunziato M, Starnone F, Giordano S, D'Antonio M, Scognamiglio D, Esposito MV, Correra A, Di Maggio F, D'Argenio V, Scaglione GL, Castaldo G, Salvatore F. One-step NGS molecular analysis of the CFTR gene on newborn dried blood spots gives a higher diagnostic sensitivity in affected and carrier subjects: A pilot study. Clin Chim Acta 2024; 552:117625. [PMID: 37923102 DOI: 10.1016/j.cca.2023.117625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Cystic fibrosis is the most common hereditary recessive disease with an incidence of about 1:2500/3000. It has long been known that the disease is caused by deleterious mutations in the CFTR gene. Conventionally, the disease is diagnosed in several phases. The analysis of all the possible disease-causing molecular alterations is time consuming and may not lead to a definitive diagnosis in several cases. Consequently, we propose, in this paper, a rapid sequencing method that, in a single procedural asset, reveals the presence of small mutations and also the copy number variants (CNVs) from the DNA extracted from the Guthrie Spot. MATERIALS AND METHODS We first sequenced 30 blood spots, then we validated the method on 100 spots that underwent both traditional analyses and this complete NGS sequencing, and lastly, we tested the strategy on patients who normally do not reach the molecular sequencing step because of low level of Immune-Reactive Trypsinogen. RESULTS Using this procedure, we identified 97 variants in the CFTR gene of our samples and 6 CNVs. Notably, the significant data were obtained in the group of patients with borderline or negative IRT who routinely would not undergo molecular testing. We also identified 6 carriers of "disease-causing" variants. CONCLUSION This method is very robust. Indeed, there was a 100% concordance with Sanger sequencing validation, and 6 mutation carriers were identified who normally escaped molecular testing with actual conventional procedure. There were also 3 duplications of almost the entire gene in heterozygosity, which were not seen with traditional methods. Being quick and easy to perform, we suggest that complete sequencing of the CFTR gene, as in this study be considered for all newborns.
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Affiliation(s)
- Marcella Nunziato
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy; CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Flavio Starnone
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy; CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Sonia Giordano
- CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Marcella D'Antonio
- CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Domenico Scognamiglio
- A.O.R.N. Santobono-Pausilipon - Centro Screening Neonatale, Via Teresa Ravaschieri già via della Croce Rossa, 8, 80122 Naples, Italy
| | - Maria Valeria Esposito
- CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Antonio Correra
- A.O.R.N. Santobono-Pausilipon - Centro Screening Neonatale, Via Teresa Ravaschieri già via della Croce Rossa, 8, 80122 Naples, Italy
| | - Federica Di Maggio
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy; CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Valeria D'Argenio
- CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy; Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Via di Val Cannuta 247, 00166 Rome, Italy
| | - Giovanni Luca Scaglione
- Istituto Dermopatico dell'Immacolata IDI-IRCCS, Via dei Monti di Creta, 104, 00167 Rome, Italy
| | - Giuseppe Castaldo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy; CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Francesco Salvatore
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy; CEINGE - Biotecnologie Avanzate Franco Salvatore, Via Gaetano Salvatore, 486, 80145 Naples, Italy.
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2
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Geng X, Tsou JH, Stass SA, Jiang F. Utilizing MiSeq Sequencing to Detect Circulating microRNAs in Plasma for Improved Lung Cancer Diagnosis. Int J Mol Sci 2023; 24:10277. [PMID: 37373422 DOI: 10.3390/ijms241210277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is a major contributor to cancer-related deaths, but early detection can reduce mortality. NSCLC comprises mainly adenocarcinoma (AC) and squamous cell carcinoma (SCC). Circulating microRNAs (miRNAs) in plasma have emerged as promising biomarkers for NSCLC. However, existing techniques for analyzing miRNAs have limitations, such as restricted target detection and time-consuming procedures. The MiSeqDx System has been shown to overcome these limitations, making it a promising tool for routine clinical settings. We investigated whether the MiSeqDx could profile cell-free circulating miRNAs in plasma and diagnose NSCLC. We sequenced RNA from the plasma of patients with AC and SCC and from cancer-free smokers using the MiSeqDx to profile and compare miRNA expressions. The MiSeqDx exhibits high speed and accuracy when globally analyzing plasma miRNAs. The entire workflow, encompassing RNA to data analysis, was completed in under three days. We also identified panels of plasma miRNA biomarkers that can diagnose NSCLC with 67% sensitivity and 68% specificity, and detect SCC with 90% sensitivity and 94% specificity, respectively. This study is the first to demonstrate that rapid profiling of plasma miRNAs using the MiSeqDx has the potential to offer a straightforward and effective method for the early detection and classification of NSCLC.
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Affiliation(s)
- Xinyan Geng
- Department of Pathology, University of Maryland School of Medicine, 10 South Pine Street, MSTF 7th Floor, Baltimore, MD 21201-1192, USA
| | - Jen-Hui Tsou
- Department of Pathology, University of Maryland School of Medicine, 10 South Pine Street, MSTF 7th Floor, Baltimore, MD 21201-1192, USA
| | - Sanford A Stass
- Department of Pathology, University of Maryland School of Medicine, 10 South Pine Street, MSTF 7th Floor, Baltimore, MD 21201-1192, USA
| | - Feng Jiang
- Department of Pathology, University of Maryland School of Medicine, 10 South Pine Street, MSTF 7th Floor, Baltimore, MD 21201-1192, USA
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Rock MJ, Baker M, Antos N, Farrell PM. Refinement of newborn screening for cystic fibrosis with next generation sequencing. Pediatr Pulmonol 2023; 58:778-787. [PMID: 36416003 DOI: 10.1002/ppul.26253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Newborn screening for cystic fibrosis (CF) has been underway universally in the United States for more than a decade, as well in most European countries, and algorithms have been evolving throughout this period with quality improvement projects as immunoreactive trypsinogen (IRT) determinations alone have been transformed to a 2-tier strategy with DNA analyses. OBJECTIVE To apply next generation sequencing (NGS) as a screening method to expand the DNA tier and identify substantially more variants in the CF transmembrane conductance regulator (CFTR) gene to enhance sensitivity and equity while minimizing incidental findings. DESIGN Sequential evaluation and improvement plan in three phases using algorithm modifications coupled to statewide follow up and analysis of screening outcomes. RESULTS After demonstrating feasibility in the first phase, we studied an IRT/NGS algorithm that included CFTR Variants with Varying Clinical Consequences (VVCCs). This revealed a high identification of CF patients with 2-variants detected through screening, but for every CF case there were 1.4 with CF metabolic syndrome/CF screen positive, inconclusive diagnosis (CRMS/CFSPID). This led us to a third phase of improvement in which the VVCCs were eliminated except for R117H, resulting in 94% 2-variant detection of patients and 0.44:1 ratio of CRMS/CFSPID to CF. CONCLUSION NGS can be used with IRT as an effective method of identifying infants at risk for CF without an appreciable increase in detection of carriers. Its potential added value includes facilitating equity, enhancing sensitivity and detecting more CF patients with 2-variants during the screening process.
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Affiliation(s)
- Michael J Rock
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Mei Baker
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.,Newborn Screening Laboratory, Wisconsin State Laboratory of Hygiene, University of Wisconsin school of Medicine and Public Health, Madison, Wisconsin, USA
| | - Nicholas Antos
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Philip M Farrell
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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Rosser JI, Tayyar R, Giardina R, Kolonoski P, Kenski D, Shen P, Steinmetz LM, Hung LY, Xiao W, Bains K, Morrison T, Madison A, Chang SI, Tompkins L, Pinsky BA, Holubar M. Case-control study evaluating risk factors for SARS-CoV-2 outbreak amongst healthcare personnel at a tertiary care center. Am J Infect Control 2021; 49:1457-1463. [PMID: 34536502 PMCID: PMC8440319 DOI: 10.1016/j.ajic.2021.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/02/2021] [Accepted: 09/08/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Despite several outbreaks of SARS-CoV-2 amongst healthcare personnel (HCP) exposed to COVID-19 patients globally, risk factors for transmission remain poorly understood. METHODS We conducted an outbreak investigation and case-control study to evaluate SARS-CoV-2 transmission risk in an outbreak among HCP at an academic medical center in California that was confirmed by whole genome sequencing. RESULTS A total of 7/9 cases and 93/182 controls completed a voluntary survey about risk factors. Compared to controls, cases reported significantly more patient contact time. Cases were also significantly more likely to have performed airway procedures on the index patient, particularly placing the patient on high flow nasal cannula, continuous positive airway pressure (CPAP), or bilevel positive airway pressure (BiPAP) (OR = 11.6; 95% CI = 1.7 -132.1). DISCUSSION This study highlights the risk of nosocomial infection of SARS-CoV-2 from patients who become infectious midway into their hospitalization. Our findings also reinforce the importance of patient contact time and aerosol-generating procedures as key risk factors for HCP infection with SARS-CoV-2. CONCLUSIONS Re-testing patients for SARS-CoV-2 after admission in suspicious cases and using N95 masks for all aerosol-generating procedures regardless of initial patient SARS-CoV-2 test results can help reduce the risk of SARS-COV-2 transmission to HCP.
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Affiliation(s)
- Joelle I Rosser
- Division of Infectious Diseases & Geographic Medicine, Stanford University School of Medicine, Stanford, CA.
| | - Ralph Tayyar
- Division of Infectious Diseases & Geographic Medicine, Stanford University School of Medicine, Stanford, CA
| | | | | | | | - Peidong Shen
- Division of Infectious Diseases & Geographic Medicine, Stanford University School of Medicine, Stanford, CA
| | - Lars M Steinmetz
- Division of Infectious Diseases & Geographic Medicine, Stanford University School of Medicine, Stanford, CA
| | - Li-Yuan Hung
- Immune-Metabolism Computational Center, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA
| | - Wenzhong Xiao
- Immune-Metabolism Computational Center, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA
| | | | | | | | | | - Lucy Tompkins
- Division of Infectious Diseases & Geographic Medicine, Stanford University School of Medicine, Stanford, CA; Stanford Health Care, Stanford, CA
| | - Benjamin A Pinsky
- Division of Infectious Diseases & Geographic Medicine, Stanford University School of Medicine, Stanford, CA
| | - Marisa Holubar
- Division of Infectious Diseases & Geographic Medicine, Stanford University School of Medicine, Stanford, CA; Stanford Health Care, Stanford, CA
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5
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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.
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Shum BOV, Bennett G, Navilebasappa A, Kumar RK. Racially equitable diagnosis of cystic fibrosis using next-generation DNA sequencing: a case report. BMC Pediatr 2021; 21:154. [PMID: 33789612 PMCID: PMC8011156 DOI: 10.1186/s12887-021-02609-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 03/11/2021] [Indexed: 12/03/2022] Open
Abstract
Background Cystic Fibrosis (CF) is one of the most prevalent autosomal recessive inherited disease in Caucasians. Rates of CF were thought to be negligible in non-Caucasians but growing epidemiological evidence shows CF is more common in Indian, African, Hispanic, Asian, and other ethnic groups than previously thought. Almost all second-tier molecular diagnostic tools currently used to confirm the diagnosis of CF consist of panels of the most common CF-causing DNA variants in Caucasians. However non-Caucasian individuals with CF often have a different spectrum of pathogenic variants than Caucasians, limiting the clinical utility of existing molecular diagnostic panels in this group. As a consequence of racially inequitable CF testing frameworks, non-Caucasians with CF encounter greater delays in diagnosis and associated harms than Caucasians. An unbiased approach of detecting CF-causing DNA variants using full gene sequencing could potentially address racial inequality in current CF testing. Case presentation We present the case of a female baby from rural India who had a borderline first-tier newborn screening result for CF. Instead of choosing a targeted CF panel for second-tier testing, we used next-generation DNA sequencing to comprehensively analyze the cystic fibrosis transmembrane conductance regulator gene as an unbiased approach for molecular confirmation of CF. Sequencing identified two pathogenic variants that cause CF. One variant (c.1521_1523delCTT) is the most common cause of CF, while the other variant (c.870-1G > C) is absent from all population allele databases and has not been found in the Indian population previously. The rare variant would not have been detected by all currently available targeted CF panels used for second- or third-tier molecular CF testing. Conclusions Our use of full gene sequencing as a second-tier CF test in a non-Caucasian patient avoided the problems of missed diagnosis from using Caucasian-biased targeted CF panels currently recommended for second-tier testing. Full gene sequencing should be considered as the standard methodology of second-tier CF testing to enable equal opportunity for CF diagnosis in non-Caucasians.
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Affiliation(s)
- Bennett O V Shum
- Preventive Health Division, Genepath, 302B 7 Help St, Chatswood, NSW, Australia. .,EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.
| | - Glenn Bennett
- Preventive Health Division, Genepath, 302B 7 Help St, Chatswood, NSW, Australia
| | | | - R Kishore Kumar
- Cloudnine Hospitals, 1533, 3rd Block, Jayanagar, Bengaluru, Karnataka, India
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McClendon-Weary B, Putnick DL, Robinson S, Yeung E. Little to Give, Much to Gain-What Can You Do With a Dried Blood Spot? Curr Environ Health Rep 2021; 7:211-221. [PMID: 32851603 DOI: 10.1007/s40572-020-00289-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Technological advances have allowed dried blood spots (DBS) to be utilized for various measurements, helpful in population-based studies. The following is a review of the literature highlighting the advantages and disadvantages of DBS and describing their use in multiple areas of research. RECENT FINDINGS DBS can track pollutant exposure to understand their impact on health. DBS can also be used for (epi-)genetic studies, to measure clinical biomarkers, and to monitor drug adherence. Advantages of DBS include being minimally invasive, requiring low blood volume, and being cost-effective to collect, transport, and store. Disadvantages of DBS include the hematocrit effect, which is related to the viscosity of the blood affecting its spread on to the filter paper, causing a major source of error when assessing concentrations, and the possibility of low DNA volume. Numerous uses for DBS make them an important source of biomaterial but they require additional validation for accuracy and reproducibility.
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Affiliation(s)
- Bryttany McClendon-Weary
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, 20817, USA
| | - Diane L Putnick
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, 20817, USA
| | - Sonia Robinson
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, 20817, USA
| | - Edwina Yeung
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, 20817, USA.
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Validation of novel forensic DNA markers using multiplex microhaplotype sequencing. Forensic Sci Int Genet 2020; 47:102275. [PMID: 32305739 PMCID: PMC10131188 DOI: 10.1016/j.fsigen.2020.102275] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/22/2020] [Accepted: 03/09/2020] [Indexed: 12/31/2022]
Abstract
Microhaplotypes (MH) are comprised of multiple single nucleotide polymorphisms (SNPs) that are located within 300 bases of genomic sequence. Improved tools are needed to facilitate broader application of microhaplotypes in a diverse range of populations and forensic settings. We designed an assay for multiplex sequencing of 90 microhaplotypes (mMHseq) that include 46 MH loci with high Effective Number of Alleles (Ae) from previous studies [1], and 44 high Ae MH loci containing between four to fourteen SNPs that were identified from the 1000 Genomes (1KG) Project. The unique design of mMHseq integrates a novel method for multiplex amplification from small DNA amounts, and multiplex sequencing of 48 samples in a single MiSeq run to detect all relevant MH variation. Assay performance was evaluated in a cohort of 156 individuals from seven different world populations from Africa, Asia, and Europe. Three of those populations from East Africa (Chagga, Sandawe, and Zaramo) and one from Eastern Europe (Adygei) had sufficient individuals sequenced by the assay to be included in statistical analyses with the 26 1KG populations. For those 30 populations the mean global average Ae was 5.08 (range: 2.7-11.54) and mean informativeness for biogeographic variation (In) was 0.30 (range: 0.08-0.70). Eighty-five novel SNPs were detected in 58 of the 90 microhaplotypes. Open-source, web-based software was developed to visualize haplotype phase data for each microhaplotype and individual. Our approach for multiplex microhaplotype sequencing can be customized and expanded as novel loci are being discovered.
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Hendrix MM, Cuthbert CD, Cordovado SK. Assessing the Performance of Dried-Blood-Spot DNA Extraction Methods in Next Generation Sequencing. Int J Neonatal Screen 2020; 6:36. [PMID: 32514487 PMCID: PMC7278269 DOI: 10.3390/ijns6020036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/27/2020] [Indexed: 12/31/2022] Open
Abstract
An increasing number of newborn screening laboratories in the United States and abroad are moving towards incorporating next-generation sequencing technology, or NGS, into routine screening, particularly for cystic fibrosis. As more programs utilize this technology for both cystic fibrosis and beyond, it is critical to identify appropriate DNA extraction methods that can be used with dried blood spots that will result in consistent, high-quality sequencing results. To provide comprehensive quality assurance and technical assistance to newborn screening laboratories wishing to incorporate NGS assays, CDC's Newborn Screening and Molecular Biology Branch designed a study to evaluate the performance of nine commercial or laboratory-developed DNA extraction methods that range from a highly purified column extraction to a crude detergent-based no-wash boil prep. The DNA from these nine methods was used in two NGS library preparations that interrogate the CFTR gene. All DNA extraction methods including the cruder preps performed reasonably well with both library preps. One lower-concentration, older sample was excluded from one of the assay evaluations due to poor performance across all DNA extraction methods. When 84 samples, versus eight, were run on a flow cell, the DNA quality and quantity were more significant variables.
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Affiliation(s)
| | | | - Suzanne K. Cordovado
- Centers for Disease Control and Prevention; 4770 Buford Hwy, NE, Atlanta, GA 30341, USA; (M.M.H.); (C.D.C.)
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10
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Bergougnoux A, Lopez M, Girodon E. The Role of Extended CFTR Gene Sequencing in Newborn Screening for Cystic Fibrosis. Int J Neonatal Screen 2020; 6:23. [PMID: 33073020 PMCID: PMC7422980 DOI: 10.3390/ijns6010023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 03/19/2020] [Indexed: 01/25/2023] Open
Abstract
There has been considerable progress in the implementation of newborn screening (NBS) programs for cystic fibrosis (CF), with DNA analysis being part of an increasing number of strategies. Thanks to advances in genomic sequencing technologies, CFTR-extended genetic analysis (EGA) by sequencing its coding regions has become affordable and has already been included as part of a limited number of core NBS programs, to the benefit of admixed populations. Based on results analysis of existing programs, the values and challenges of EGA are reviewed in the perspective of its implementation on a larger scale. Sensitivity would be increased at best by using EGA as a second tier, but this could be at the expense of positive predictive value, which improves, however, if EGA is applied after testing a variant panel. The increased detection of babies with an inconclusive diagnosis has proved to be a major drawback in programs using EGA. The lack of knowledge on pathogenicity and penetrance associated with numerous variants hinders the introduction of EGA as a second tier, but EGA with filtering for all known CF variants with full penetrance could be a solution. The issue of incomplete knowledge is a real challenge in terms of the implemention of NBS extended to many genetic diseases.
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Affiliation(s)
- Anne Bergougnoux
- Molecular Genetics Laboratory, CHU Montpellier, EA7402 University of Montpellier, 34093 Montpellier CEDEX 5, France;
| | - Maureen Lopez
- Molecular Genetics Laboratory, Cochin Hospital, APHP. Centre, University of Paris, 75014 Paris, France;
| | - Emmanuelle Girodon
- Molecular Genetics Laboratory, Cochin Hospital, APHP. Centre, University of Paris, 75014 Paris, France;
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Ivanov M, Ivanov M, Kasianov A, Rozhavskaya E, Musienko S, Baranova A, Mileyko V. Novel bioinformatics quality control metric for next-generation sequencing experiments in the clinical context. Nucleic Acids Res 2019; 47:e135. [PMID: 31511888 PMCID: PMC6868350 DOI: 10.1093/nar/gkz775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 07/22/2019] [Accepted: 08/29/2019] [Indexed: 11/23/2022] Open
Abstract
As the use of next-generation sequencing (NGS) for the Mendelian diseases diagnosis is expanding, the performance of this method has to be improved in order to achieve higher quality. Typically, performance measures are considered to be designed in the context of each application and, therefore, account for a spectrum of clinically relevant variants. We present EphaGen, a new computational methodology for bioinformatics quality control (QC). Given a single NGS dataset in BAM format and a pre-compiled VCF-file of targeted clinically relevant variants it associates this dataset with a single arbiter parameter. Intrinsically, EphaGen estimates the probability to miss any variant from the defined spectrum within a particular NGS dataset. Such performance measure virtually resembles the diagnostic sensitivity of given NGS dataset. Here we present case studies of the use of EphaGen in context of BRCA1/2 and CFTR sequencing in a series of 14 runs across 43 blood samples and 504 publically available NGS datasets. EphaGen is superior to conventional bioinformatics metrics such as coverage depth and coverage uniformity. We recommend using this software as a QC step in NGS studies in the clinical context. Availability: https://github.com/m4merg/EphaGen or https://hub.docker.com/r/m4merg/ephagen.
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Affiliation(s)
- Maxim Ivanov
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Mikhail Ivanov
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Artem Kasianov
- Vavilov Institute of General Genetics, Moscow, Russian Federation
| | - Ekaterina Rozhavskaya
- Vavilov Institute of General Genetics, Moscow, Russian Federation.,Atlas Oncology Diagnostics, Ltd, Moscow, Russian Federation
| | | | - Ancha Baranova
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation.,Atlas Oncology Diagnostics, Ltd, Moscow, Russian Federation.,Research Centre for Medical Genetics, Moscow, Russian Federation.,School of Systems Biology, George Mason University, Fairfax, VA 22030, USA
| | - Vladislav Mileyko
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation.,Atlas Oncology Diagnostics, Ltd, Moscow, Russian Federation
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12
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Strunk A, Abbes A, Stuitje AR, Hettinga C, Sepers EM, Snetselaar R, Schouten J, Asselman FL, Cuppen I, Lemmink H, van der Pol WL, Engel H. Validation of a Fast, Robust, Inexpensive, Two-Tiered Neonatal Screening Test algorithm on Dried Blood Spots for Spinal Muscular Atrophy. Int J Neonatal Screen 2019; 5:21. [PMID: 33072980 PMCID: PMC7510214 DOI: 10.3390/ijns5020021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/13/2019] [Indexed: 11/16/2022] Open
Abstract
Spinal muscular atrophy (SMA) is one of the leading genetic causes of infant mortality with an incidence of 1:10,000. The recently-introduced antisense oligonucleotide treatment improves the outcome of this disease, in particular when applied at an early stage of progression. The genetic cause of SMA is, in >95% of cases, a homozygous deletion of the survival motor neuron 1 (SMN1) gene, which makes the low-cost detection of SMA cases as part of newborn screening programs feasible. We developed and validated a new SALSA MC002 melting curve assay that detects the absence of the SMN1 exon 7 DNA sequence without detecting asymptomatic carriers and reliably discriminates SMN1 from its genetic homolog SMN2 using crude extracts from newborn screening cards. Melting curve analysis shows peaks specific for both the SMN1 gene and the disease modifying SMN2 homolog. The detection of the SMN2 homolog, of which the only clinically relevant difference from the SMN1 gene is a single nucleotide in exon 7, was only used to confirm a correct reaction in samples that lacked the SMN1 gene, and not for SMN2 quantification. We retrieved 47 DBS samples from children with genetically-confirmed SMA, after informed consent from parents, and 375 controls from the national archive of the Dutch National Institute for Public Health and the Environment (RIVM). The assay correctly identified all anonymized and randomized SMA and control samples (i.e., sensitivity and specificity of 100%), without the detection of carriers, on the three most commonly-used PCR platforms with melting curve analysis. This test's concordance with the second-tier 'golden standard' P021 SMA MLPA test was 100%. Using the new P021-B1 version, crude extracts from DBS cards could also be used to determine the SMN2 copy number of SMA patients with a high level of accuracy. The MC002 test showed the feasibility and accuracy of SMA screening in a neonatal screening program.
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Affiliation(s)
- Annuska Strunk
- Department of Clinical Chemistry and Neonatal Screening, Isala Hospital, Dokter van Heesweg 2, 8025 AB Zwolle, The Netherlands
| | - Andre Abbes
- Department of Clinical Chemistry and Neonatal Screening, Isala Hospital, Dokter van Heesweg 2, 8025 AB Zwolle, The Netherlands
| | - Antoine R. Stuitje
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Chris Hettinga
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Eline M. Sepers
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Reinier Snetselaar
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Jan Schouten
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Fay-Lynn Asselman
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Inge Cuppen
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Henny Lemmink
- Department of Genetics, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - W. Ludo van der Pol
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Henk Engel
- Department of Clinical Chemistry and Neonatal Screening, Isala Hospital, Dokter van Heesweg 2, 8025 AB Zwolle, The Netherlands
- Correspondence: ; Tel.: +31-38-424-7190
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13
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DiBattista A, McIntosh N, Lamoureux M, Al-Dirbashi OY, Chakraborty P, Britz-McKibbin P. Metabolic Signatures of Cystic Fibrosis Identified in Dried Blood Spots For Newborn Screening Without Carrier Identification. J Proteome Res 2019; 18:841-854. [PMID: 30507207 DOI: 10.1021/acs.jproteome.8b00351] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cystic fibrosis (CF) is a complex multiorgan disorder that is among the most common fatal genetic diseases benefiting from therapeutic interventions early in life. Newborn screening (NBS) for presymptomatic detection of CF currently relies on a two-stage immunoreactive trypsinogen (IRT) and cystic fibrosis transmembrane conductance regulator (CFTR) mutation panel algorithm that is sensitive but not specific for identifying affected neonates with a low positive predictive value. For the first time, we report the discovery of a panel of CF-specific metabolites from a single 3.2 mm diameter dried blood spot (DBS) punch when using multisegment injection-capillary electrophoresis-mass spectrometry (MS) as a high-throughput platform for nontargeted metabolite profiling from volume-restricted/biobanked specimens with quality control. This retrospective case-control study design identified 32 metabolites, including a series of N-glycated amino acids, oxidized glutathione disulfide, and nicotinamide that were differentially expressed in normal birth weight CF neonates without meconium ileus ( n = 36) as compared to gestational age/sex-matched screen-negative controls ( n = 44) after a false discovery rate adjustment ( q < 0.05). Also, 16 metabolites from DBS extracts allowed for discrimination of true CF cases from presumptive screen-positive carriers with one identified CFTR mutation and transient neonatal hypertrypsinogenemic neonates ( n = 72), who were later confirmed as unaffected due to a low sweat chloride (<29 mM) test result. Importantly, six CF-specific biomarker candidates satisfying a Bonferroni adjustment ( p < 7.25 × 10-5) from three independent batches of DBS specimens included several amino acids depleted in circulation (Tyr, Ser, Thr, Pro, Gly) likely reflecting protein maldigestion/malabsorption. Additionally, CF neonates had lower ophthalmic acid as an indicator of oxidative stress due to impaired glutathione efflux from exocrine/epithelial tissue and elevation of an unknown trivalent peptide that was directly correlated with IRT (ρ = 0.332, p = 4.55 × 10-4). Structural elucidation of unknown metabolites was performed by high-resolution MS/MS, whereas biomarker validation was realized when comparing a subset of metabolites from matching neonatal DBS specimens independently analyzed by direct infusion-MS/MS at an accredited NBS facility. This work sheds new light into the metabolic phenotype of CF early in life, which is required for better functional understanding of CFTR mutations of unknown clinical consequence and the development of more accurate yet cost-effective strategies for CF screening.
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Affiliation(s)
- Alicia DiBattista
- Department of Chemistry and Chemical Biology , McMaster University , Hamilton L8S 4M1 , Canada
| | | | | | - Osama Y Al-Dirbashi
- College of Medicine and Health Sciences , United Arab Emirates University , Al Ain 15551 , United Arab Emirates
| | | | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology , McMaster University , Hamilton L8S 4M1 , Canada
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14
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Peng G, Shen P, Gandotra N, Le A, Fung E, Jelliffe-Pawlowski L, Davis RW, Enns GM, Zhao H, Cowan TM, Scharfe C. Combining newborn metabolic and DNA analysis for second-tier testing of methylmalonic acidemia. Genet Med 2018; 21:896-903. [PMID: 30209273 PMCID: PMC6416784 DOI: 10.1038/s41436-018-0272-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/03/2018] [Indexed: 11/27/2022] Open
Abstract
Purpose Improved second-tier tools are needed to reduce false-positive outcomes in newborn screening (NBS) for inborn metabolic disorders on the Recommended Universal Screening Panel (RUSP). Methods We designed an assay for multiplex sequencing of 72 metabolic genes (RUSPseq) from newborn dried blood spots. Analytical and clinical performance was evaluated in 60 screen-positive newborns for methylmalonic acidemia (MMA) reported by the California Department of Public Health NBS program. Additionally, we trained a Random Forest machine learning classifier on NBS data to improve prediction of true and false-positive MMA cases. Results Of 28 MMA patients sequenced, we found two pathogenic or likely pathogenic (P/LP) variants in a MMA-related gene in 24 patients, and one pathogenic variant and a variant of unknown significance (VUS) in 1 patient. No such variant combinations were detected in MMA false positives and healthy controls. Random Forest–based analysis of the entire NBS metabolic profile correctly identified the MMA patients and reduced MMA false-positive cases by 51%. MMA screen-positive newborns were more likely of Hispanic ethnicity. Conclusion Our two-pronged approach reduced false positives by half and provided a reportable molecular finding for 89% of MMA patients. Challenges remain in newborn metabolic screening and DNA variant interpretation in diverse multiethnic populations.
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Affiliation(s)
- Gang Peng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Peidong Shen
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Neeru Gandotra
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Anthony Le
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eula Fung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Jelliffe-Pawlowski
- Department of Epidemiology and Biostatistics, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Ronald W Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Gregory M Enns
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Tina M Cowan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Curt Scharfe
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
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15
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Abstract
Identifying mutations that cause cystic fibrosis (CF) is important for making an early, unambiguous diagnosis, which, in turn, is linked to better health and a greater life expectancy. In patients of African descent, a molecular diagnosis is often confounded by the fact that the majority of investigations undertaken to identify causative mutations have been conducted on European populations, and CF-causing mutations tend to be population specific. We undertook a survey of published data with the aim of identifying causative CF mutations in patients of African descent in the Americas. We found that 1,584 chromosomes had been tested in only 6 countries, of which 876 alleles (55.3%) still remained unidentified. There were 59 mutations identified. Of those, 41 have been shown to cause CF, 17 have no associated functional studies, and one (R117H) is of varying clinical consequence. The most common mutations identified in the patients of African descent were: ΔF508 (29.4% identified in the United States, Colombia, Brazil, and Venezuela); 3120 + 1G>A (8.4% identified in Brazil, the United States, and Colombia); G85E (3.8% identified in Brazil); 1811 + 1.6kbA>G (3.7% identified in Colombia); and 1342 - 1G>C (3.1% identified in the United States). The majority of the mutations identified (81.4%) have been described in just one country. Our findings indicate that there is a need to fully characterize the spectrum of CF mutations in the diaspora to improve diagnostic accuracy for these patients and facilitate treatment.
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16
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Durie D, Yeh E, McIntosh N, Fisher L, Bulman DE, Birnboim HC, Chakraborty P, Al-Dirbashi OY. Quantification of DNA in Neonatal Dried Blood Spots by Adenine Tandem Mass Spectrometry. Anal Chem 2017; 90:801-806. [PMID: 29190072 DOI: 10.1021/acs.analchem.7b03265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Newborn screening programs have expanded to include molecular-based assays as first-tier tests and the success of these assays depends on the quality and yield of DNA extracted from neonatal dried blood spots (DBS). To meet high throughput and rapid turnaround time requirements, newborn screening laboratories adopted rapid DNA extraction methods that produce crude extracts. Quantification of DNA in neonatal DBS is not routinely performed due to technical challenges; however, this may enhance the performance of assays that are sensitive to amounts of input DNA. In this study, we developed a novel high throughput method to quantify total DNA in DBS. It is based on specific acid-catalyzed depurination of DNA followed by mass spectrometric quantification of adenine. The amount of adenine was used to calculate DNA quantity per 3.2 mm DBS. Reference intervals were established using archived, neonatal DBS (n = 501) and a median of 130.6 ng of DNA per DBS was obtained, which is in agreement with literature values. The intra- and interday variations were <15%. The limits of detection and quantification were 12.5 and 37.8 nmol/L adenine, respectively. We demonstrated that DNA from neonatal DBS can be successfully quantified in high throughput settings using instruments currently deployed in NBS laboratories.
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Affiliation(s)
- Danielle Durie
- Newborn Screening Ontario, Ottawa, Ontario K1H 8L1, Canada
| | - Ed Yeh
- Newborn Screening Ontario, Ottawa, Ontario K1H 8L1, Canada
| | | | | | - Dennis E Bulman
- Newborn Screening Ontario, Ottawa, Ontario K1H 8L1, Canada.,Department of Pediatrics, University of Ottawa , Ottawa, Ontario K1H8M5, Canada.,Ottawa Hospital Research Institute , Ottawa, Ontario K1H 8L6, Canada.,Research Institute, Children's Hospital of Eastern Ontario , Ottawa, Ontario K1H 5B2, Canada
| | | | - Pranesh Chakraborty
- Newborn Screening Ontario, Ottawa, Ontario K1H 8L1, Canada.,Department of Pediatrics, University of Ottawa , Ottawa, Ontario K1H8M5, Canada.,Research Institute, Children's Hospital of Eastern Ontario , Ottawa, Ontario K1H 5B2, Canada
| | - Osama Y Al-Dirbashi
- Newborn Screening Ontario, Ottawa, Ontario K1H 8L1, Canada.,Research Institute, Children's Hospital of Eastern Ontario , Ottawa, Ontario K1H 5B2, Canada.,College of Medicine and Health Sciences, United Arab Emirates University , Al Ain, 17172, United Arab Emirates
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17
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Cho Y, Lee CH, Jeong EG, Kim MH, Hong JH, Ko Y, Lee B, Yun G, Kim BJ, Jung J, Jung J, Lee JS. Prevalence of Rare Genetic Variations and Their Implications in NGS-data Interpretation. Sci Rep 2017; 7:9810. [PMID: 28851938 PMCID: PMC5574920 DOI: 10.1038/s41598-017-09247-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 07/21/2017] [Indexed: 12/30/2022] Open
Abstract
Next-generation sequencing (NGS) technology has improved enough to discover mutations associated with genetic diseases. Our study evaluated the feasibility of targeted NGS as a primary screening tool to detect causal variants and subsequently predict genetic diseases. We performed parallel computations on 3.7-megabase-targeted regions to detect disease-causing mutations in 103 participants consisting of 81 patients and 22 controls. Data analysis of the participants took about 6 hours using local databases and 200 nodes of a supercomputer. All variants in the selected genes led on average to 3.6 putative diseases for each patient while variants restricted to disease-causing genes identified the correct disease. Notably, only 12% of predicted causal variants were recorded as causal mutations in public databases: 88% had no or insufficient records. In this study, most genetic diseases were caused by rare mutations and public records were inadequate. Most rare variants, however, were not associated with genetic diseases. These data implied that novel, rare variants should not be ignored but interpreted in conjunction with additional clinical data. This step is needed so appropriate advice can be given to primary doctors and parents, thus fulfilling the purpose of this method as a primary screen for rare genetic diseases.
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Affiliation(s)
- Yangrae Cho
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
- DFTBA, CALS, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Chul-Ho Lee
- Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Eun-Goo Jeong
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Min-Ho Kim
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Jong Hui Hong
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Younhee Ko
- Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Department of Biomedical Engineering, Hankuk University of Foreign Studies, Yongin-si, Gyeonggi-do, 17035, Republic of Korea
| | - Bomnun Lee
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Gilly Yun
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Byong Joon Kim
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Jongcheol Jung
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Jongsun Jung
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea.
| | - Jin-Sung Lee
- Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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18
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Lucarelli M, Porcaro L, Biffignandi A, Costantino L, Giannone V, Alberti L, Bruno SM, Corbetta C, Torresani E, Colombo C, Seia M. A New Targeted CFTR Mutation Panel Based on Next-Generation Sequencing Technology. J Mol Diagn 2017; 19:788-800. [PMID: 28736296 DOI: 10.1016/j.jmoldx.2017.06.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 06/01/2017] [Accepted: 06/07/2017] [Indexed: 01/16/2023] Open
Abstract
Searching for mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) is a key step in the diagnosis of and neonatal and carrier screening for cystic fibrosis (CF), and it has implications for prognosis and personalized therapy. The large number of mutations and genetic and phenotypic variability make this search a complex task. Herein, we developed, validated, and tested a laboratory assay for an extended search for mutations in CFTR using a next-generation sequencing-based method, with a panel of 188 CFTR mutations customized for the Italian population. Overall, 1426 dried blood spots from neonatal screening, 402 genomic DNA samples from various origins, and 1138 genomic DNA samples from patients with CF were analyzed. The assay showed excellent analytical and diagnostic operative characteristics. We identified and experimentally validated 159 (of 188) CFTR mutations. The assay achieved detection rates of 95.0% and 95.6% in two large-scale case series of CF patients from central and northern Italy, respectively. These detection rates are among the highest reported so far with a genetic test for CF based on a mutation panel. This assay appears to be well suited for diagnostics, neonatal and carrier screening, and assisted reproduction, and it represents a considerable advantage in CF genetic counseling.
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Affiliation(s)
- Marco Lucarelli
- Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy; Pasteur Institute Cenci Bolognetti Foundation, Sapienza University, Rome, Italy.
| | - Luigi Porcaro
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alice Biffignandi
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lucy Costantino
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Giannone
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luisella Alberti
- Newborn Screening Laboratory, ASST Fatebenefratelli Sacco-PO Ospedale dei Bambini "V. Buzzi", Milan, Italy
| | - Sabina Maria Bruno
- Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Carlo Corbetta
- Newborn Screening Laboratory, ASST Fatebenefratelli Sacco-PO Ospedale dei Bambini "V. Buzzi", Milan, Italy
| | - Erminio Torresani
- Unit of Microbiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Carla Colombo
- Cystic Fibrosis Centre, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Manuela Seia
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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19
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Jang JH, Lee T, Bang S, Kim YE, Cho EH. Carrier frequency of Wilson's disease in the Korean population: a DNA-based approach. J Hum Genet 2017; 62:815-818. [PMID: 28515472 DOI: 10.1038/jhg.2017.49] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/28/2017] [Accepted: 04/02/2017] [Indexed: 01/10/2023]
Abstract
Wilson's disease (WD) is an autosomal recessive disorder caused by ATP7B gene mutation. The frequency of WD is about 1 in 30 000 worldwide. In the present study, we screened 14 835 dried blood spots (DBSs) from asymptomatic Korean neonates and retrospectively reviewed massively parallel sequencing of 1090 control individuals to estimate carrier frequency. TaqMan real-time PCR assays were conducted to detect six mutations that account for 58.3% of mutations in Korean WD patients: c.2333G>T (p.Arg778Leu), c.2621C>T (p.Ala874Val), c.3086C>T (p.Thr1029Ile), c.3247C>T (p.Leu1083Phe), c.3556G>A (p.Gly1186Ser) and c.3809A>G (p.Asn1270Ser). We also retrospectively reviewed data from 1090 individuals with various indications other than WD for whom whole-exome or panel sequencing data were available. Mutant allele frequency based on the six most common mutations was 0.0067 among the total of 14 835 DBSs screened. Given that these six mutations account for 58.3% of mutations in Korean WD patients, the corrected mutant allele frequency is 0.0115 (95% confidence interval (CI): 0.0103-0.0128). Corresponding incidence (q2) and carrier frequency (2pq) were estimated to be 1:7561 and 1:44, respectively. In retrospective data analysis of 1090 control individuals, allele frequency of pathogenic or likely pathogenic variants was 0.0096 (95% CI: 0.0063-0.0146). Corresponding carrier frequency was estimated to be 1:53. Estimated allele and carrier frequencies based on DNA screening were relatively higher than those reported previously based on clinical ascertainment.
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Affiliation(s)
- Ja-Hyun Jang
- Genome Research Center, Green Cross Genome, Yong-in, Republic of Korea.,Green Cross Laboratories, Yong-in, Republic of Korea
| | - Taeheon Lee
- Genome Research Center, Green Cross Genome, Yong-in, Republic of Korea
| | - Sunghee Bang
- Genome Research Center, Green Cross Genome, Yong-in, Republic of Korea
| | - Young-Eun Kim
- Genome Research Center, Green Cross Genome, Yong-in, Republic of Korea.,Green Cross Laboratories, Yong-in, Republic of Korea
| | - Eun-Hae Cho
- Genome Research Center, Green Cross Genome, Yong-in, Republic of Korea
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20
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Genomic sequencing in cystic fibrosis newborn screening: what works best, two-tier predefined CFTR mutation panels or second-tier CFTR panel followed by third-tier sequencing? Genet Med 2017; 19:1159-1163. [PMID: 28471435 DOI: 10.1038/gim.2017.32] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 02/06/2017] [Accepted: 02/09/2017] [Indexed: 01/08/2023] Open
Abstract
PurposeThe purpose of this study was to model the performance of several known two-tier, predefined mutation panels and three-tier algorithms for cystic fibrosis (CF) screening utilizing the ethnically diverse California population.MethodsThe cystic fibrosis transmembrane conductance regulator (CFTR) mutations identified among the 317 CF cases in California screened between 12 August 2008 and 18 December 2012 were used to compare the expected CF detection rates for several two- and three-tier screening approaches, including the current California approach, which consists of a population-specific 40-mutation panel followed by third-tier sequencing when indicated.ResultsThe data show that the strategy of using third-tier sequencing improves CF detection following an initial elevated immunoreactive trypsinogen and detection of only one mutation on a second-tier panel.ConclusionIn a diverse population, the use of a second-tier panel followed by third-tier CFTR gene sequencing provides a better detection rate for CF, compared with the use of a second-tier approach alone, and is an effective way to minimize the referrals of CF carriers for sweat testing. Restricting screening to a second-tier testing to predefined mutation panels, even broad ones, results in some missed CF cases and demonstrates the limited utility of this approach in states that have diverse multiethnic populations.
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21
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Lucarelli M. New era of cystic fibrosis: Full mutational analysis and personalized therapy. World J Med Genet 2017; 7:1-9. [DOI: 10.5496/wjmg.v7.i1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/19/2016] [Accepted: 02/21/2017] [Indexed: 02/07/2023] Open
Abstract
Despite its apparently simple genetics, cystic fibrosis (CF) is a rather complex genetic disease. A lot of variability in the steps of the path from the cystic fibrosis transmembrane conductance regulator (CFTR) gene to the clinical manifestations originates an uncertain genotype - phenotype relationship. A major determinant of this uncertainty is the incomplete knowledge of the CFTR mutated genotypes, due to the high number of CFTR mutations and to the higher number of their combinations in trans and in cis. Also the very limited knowledge of functional effects of CFTR mutated alleles severely impairs our diagnostic and prognostic ability. The final phenotypic modulation exerted by CFTR modifier genes and interactome further complicates the framework. The next generation sequencing approach is a rapid, low-cost and high-throughput tool that allows a near complete structural characterization of CFTR mutated genotypes, as well as of genotypes of several other genes cooperating to the final CF clinical manifestations. This powerful method perfectly complements the new personalized therapeutic approach for CF. Drugs active on specific CFTR mutational classes are already available for CF patients or are in phase 3 trials. A complete genetic characterization has been becoming crucial for a correct personalized therapy. However, the need of a functional classification of each CFTR mutation potently arises. Future big efforts towards an ever more detailed knowledge of both structural and functional CFTR defects, coupled to parallel personalized therapeutic interventions decisive for CF cure can be foreseen.
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Affiliation(s)
- Marco Lucarelli
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00161 Rome, Italy
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22
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Sweat chloride testing: controversies and issues. THE LANCET RESPIRATORY MEDICINE 2016; 4:605-607. [DOI: 10.1016/s2213-2600(16)30182-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 06/21/2016] [Indexed: 11/23/2022]
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23
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Pique L, Graham S, Pearl M, Kharrazi M, Schrijver I. Cystic fibrosis newborn screening programs: implications of the CFTR variant spectrum in nonwhite patients. Genet Med 2016; 19:36-44. [DOI: 10.1038/gim.2016.48] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 03/08/2016] [Indexed: 11/10/2022] Open
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24
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The Challenges of Applying Massively Parallel Sequencing to Newborn Screening for Cystic Fibrosis. J Mol Diagn 2016; 18:163-4. [PMID: 26874346 DOI: 10.1016/j.jmoldx.2015.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 12/28/2015] [Accepted: 12/30/2015] [Indexed: 11/24/2022] Open
Abstract
This Commentary highlights the article by Lefterova et al that describes newborn screening of cystic fibrosis using massively parallel sequencing.
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Hendrix MM, Foster SL, Cordovado SK. Newborn Screening Quality Assurance Program for CFTR Mutation Detection and Gene Sequencing to Identify Cystic Fibrosis. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2016; 4. [PMID: 28261631 PMCID: PMC5332130 DOI: 10.1177/2326409816661358] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
All newborn screening laboratories in the United States and many worldwide screen for cystic fibrosis. Most laboratories use a second-tier genotyping assay to identify a panel of mutations in the CF transmembrane regulator (CFTR) gene. Centers for Disease Control and Prevention’s Newborn Screening Quality Assurance Program houses a dried blood spot repository of samples containing CFTR mutations to assist newborn screening laboratories and ensure high-quality mutation detection in a high-throughput environment. Recently, CFTR mutation detection has increased in complexity with expanded genotyping panels and gene sequencing. To accommodate the growing quality assurance needs, the repository samples were characterized with several multiplex genotyping methods, Sanger sequencing, and 3 next-generation sequencing assays using a high-throughput, low-concentration DNA extraction method. The samples performed well in all of the assays, providing newborn screening laboratories with a resource for complex CFTR mutation detection and next-generation sequencing as they transition to new methods.
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