1
|
Thomas SP, Fletcher FE, Willard R, Ranson TM, Bonham VL. Patient Perceptions on the Advancement of Noninvasive Prenatal Testing for Sickle Cell Disease among Black Women in the United States. AJOB Empir Bioeth 2024; 15:154-163. [PMID: 38349128 DOI: 10.1080/23294515.2024.2302996] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
BACKGROUND Noninvasive prenatal testing (NIPT) designed to screen for fetal genetic conditions, is increasingly being implemented as a part of routine prenatal care screening in the United States (US). However, these advances in reproductive genetic technology necessitate empirical research on the ethical and social implications of NIPT among populations underrepresented in genetic research, particularly Black women with sickle cell disease (SCD). METHODS Forty (N = 40) semi-structured interviews were conducted virtually with Black women in the US (19 participants with SCD; 21 participants without SCD) from June 2021 to January 2022. We employed a qualitative approach to examine the study participants' perceptions of the potential advancement of NIPT for screening SCD in the fetus. Data were analyzed using NVivo 12 qualitative software. RESULTS The themes revealed the complexities involving the intersectional lived experiences of SCD, prenatal care, lack of synergy among health providers, and NIPT decision-making. The results further revealed that even when Black women have shared commonalities in their lived experiences while navigating SCD and motherhood, their perceptions of NIPT screening technologies are divergent. CONCLUSION Expanding the ethical discourse on the social implications of NIPT is critical to fully elucidate how Black women perceive NIPT's utility, particularly as NIPT advances to screen for SCD in the fetus. Neglecting to include Black women with genetic conditions in empirical studies on NIPT may contribute to ongoing health inequities and limit and constrain reproductive choices among Black women with and without SCD.
Collapse
Affiliation(s)
- Shameka P Thomas
- School of Public Health, Harvard University, Boston, Massachusetts, USA
- National Institutes of Health-National Genome Research Institute, Bethesda, Maryland, USA
| | - Faith E Fletcher
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Rachele Willard
- National Institutes of Health-National Genome Research Institute, Bethesda, Maryland, USA
| | - Tiara Monet Ranson
- National Institutes of Health-National Genome Research Institute, Bethesda, Maryland, USA
- School of Public Health, University of Washington, Washington, Seattle, USA
| | - Vence L Bonham
- National Institutes of Health-National Genome Research Institute, Bethesda, Maryland, USA
| |
Collapse
|
2
|
Ally M, Balandya E. Current challenges and new approaches to implementing optimal management of sickle cell disease in sub-Saharan Africa. Semin Hematol 2023; 60:192-199. [PMID: 37730472 PMCID: PMC10909340 DOI: 10.1053/j.seminhematol.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/01/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023]
Abstract
Sickle cell disease (SCD) is the most common life-threatening monogenic disorder in the world. The disease is highly prevalent in malaria endemic areas with over 75% of patients residing in Sub-Saharan Africa (SSA). It is estimated that, without proper care, up to 90% of children with SCD will not celebrate their fifth birthday. Early identification and enrolment into comprehensive care has been shown to reduce the morbidity and mortality related with SCD complications. However, due to resource constraints, the SSA is yet to implement universal newborn screening programs for SCD. Furthermore, care for patients with SCD in the region is hampered by the shortage of qualified healthcare workers, lack of guidelines for the clinical management of SCD, limited infrastructure for inpatient and outpatient care, and limited access to blood and disease modifying drugs such as Hydroxyurea which contribute to poor clinical outcomes. Curative options such as bone marrow transplant and gene therapy are expensive and not available in many SSA countries. In addressing these challenges, various initiatives are ongoing in SSA which aim to enhance awareness on SCD, improve patient identification and retention to care, harmonize the standards of care for SCD, improve the skills of healthcare workers and conduct research on pertinent areas in SCD in the SSA context. Fortifying these measures is paramount to improving the outcomes of SCD in SSA.
Collapse
Affiliation(s)
- Mwashungi Ally
- Sickle Pan African Research Consortium, Tanzania site Sickle Cell Program Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences Dar es Salaam Tanzania.
| | - Emmanuel Balandya
- Sickle Pan African Research Consortium, Tanzania site Sickle Cell Program Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences Dar es Salaam Tanzania
| |
Collapse
|
3
|
Shaw J, Scotchman E, Paternoster B, Ramos M, Nesbitt S, Sheppard S, Snowsill T, Chitty LS, Chandler N. Non-invasive fetal genotyping for maternal alleles with droplet digital PCR: A comparative study of analytical approaches. Prenat Diagn 2023; 43:477-488. [PMID: 36760169 DOI: 10.1002/pd.6333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/22/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
OBJECTIVES To develop a flexible droplet digital PCR (ddPCR) workflow to perform non-invasive prenatal diagnosis via relative mutation dosage (RMD) for maternal pathogenic variants with a range of inheritance patterns, and to compare the accuracy of multiple analytical approaches. METHODS Cell free DNA (cfDNA) was tested from 124 archived maternal plasma samples: 88 cases for sickle cell disease and 36 for rare Mendelian conditions. Three analytical methods were compared: sequential probability ratio testing (SPRT), Bayesian and z-score analyses. RESULTS The SPRT, Bayesian and z-score analyses performed similarly well with correct prediction rates of 96%, 97% and 98%, respectively. However, there were high rates of inconclusive results for each cohort, particularly for z-score analysis which was 31% overall. Two samples were incorrectly classified by all three analytical methods; a false negative result predicted for a fetus affected with sickle cell disease and a false positive result predicting the presence of an X-linked IDS variant in an unaffected fetus. CONCLUSIONS ddPCR can be applied to RMD for diverse conditions and inheritance patterns, but all methods carry a small risk of erroneous results. Further evaluation is required both to reduce the rate of inconclusive results and explore discordant results in more detail.
Collapse
Affiliation(s)
- Joe Shaw
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Ben Paternoster
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Maureen Ramos
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Sarah Nesbitt
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Sophie Sheppard
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | | | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Natalie Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| |
Collapse
|
4
|
Hanson B, Scotchman E, Chitty LS, Chandler NJ. Non-invasive prenatal diagnosis (NIPD): how analysis of cell-free DNA in maternal plasma has changed prenatal diagnosis for monogenic disorders. Clin Sci (Lond) 2022; 136:1615-1629. [PMID: 36383187 PMCID: PMC9670272 DOI: 10.1042/cs20210380] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 07/30/2023]
Abstract
Cell-free fetal DNA (cffDNA) is released into the maternal circulation from trophoblastic cells during pregnancy, is detectable from 4 weeks and is representative of the entire fetal genome. The presence of this cffDNA in the maternal bloodstream has enabled clinical implementation of non-invasive prenatal diagnosis (NIPD) for monogenic disorders. Detection of paternally inherited and de novo mutations is relatively straightforward, and several methods have been developed for clinical use, including quantitative polymerase chain reaction (qPCR), and PCR followed by restriction enzyme digest (PCR-RED) or next-generation sequencing (NGS). A greater challenge has been in the detection of maternally inherited variants owing to the high background of maternal cell-free DNA (cfDNA). Molecular counting techniques have been developed to measure subtle changes in allele frequency. For instance, relative haplotype dosage analysis (RHDO), which uses single nucleotide polymorphisms (SNPs) for phasing of high- and low-risk alleles, is clinically available for several monogenic disorders. A major drawback is that RHDO requires samples from both parents and an affected or unaffected proband, therefore alternative methods, such as proband-free RHDO and relative mutation dosage (RMD), are being investigated. cffDNA was thought to exist only as short fragments (<500 bp); however, long-read sequencing technologies have recently revealed a range of sizes up to ∼23 kb. cffDNA also carries a specific placental epigenetic mark, and so fragmentomics and epigenetics are of interest for targeted enrichment of cffDNA. Cell-based NIPD approaches are also currently under investigation as a means to obtain a pure source of intact fetal genomic DNA.
Collapse
Affiliation(s)
- Britt Hanson
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| | - Lyn S. Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
- Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, U.K
| | - Natalie J. Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| |
Collapse
|
5
|
Erlich HA, López-Peña C, Carlberg KT, Shih S, Bali G, Yamaguchi KD, Salamon H, Das R, Lal A, Calloway CD. Non-Invasive Prenatal Test for β-Thalassemia and Sickle Cell Disease Using Probe Capture Enrichment and Next-Generation Sequencing of DNA in Maternal Plasma. J Appl Lab Med 2021; 7:515-531. [PMID: 34849992 DOI: 10.1093/jalm/jfab118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/30/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND Noninvasive prenatal testing (NIPT) of chromosomal aneuploidies based on next-generation sequencing (NGS) analysis of fetal DNA in maternal plasma is well established, but testing for autosomal recessive disorders remains challenging. NGS libraries prepared by probe capture facilitate the analysis of the short DNA fragments plasma. This system has been applied to the β-hemoglobinopathies to reduce the risk to the fetus. METHOD Our probe panel captures >4 kb of the HBB region and 435 single-nucleotide polymorphisms (SNPs) used to estimate fetal fraction. Contrived mixtures of DNA samples, plasma, and whole blood samples from 7 pregnant women with β-thalassemia or sickle cell anemia mutations and samples from the father, sibling, and baby or chorionic villus were analyzed. The fetal genotypes, including point mutations and deletions, were inferred by comparing the observed and expected plasma sequence read ratios, based on fetal fraction, at the mutation site and linked SNPs. Accuracy was increased by removing PCR duplicates and by in silico size selection of plasma sequence reads. A probability was assigned to each of the potential fetal genotypes using a statistical model for the experimental variation, and thresholds were established for assigning clinical status. RESULTS Using in silico size selection of plasma sequence files, the predicted clinical fetal genotype assignments were correct in 9 of 10 plasma libraries with maternal point mutations, with 1 inconclusive result. For 2 additional plasmas with deletions, the most probable fetal genotype was correct. The β-globin haplotype determined from linked SNPs, when available, was used to infer the fetal genotype at the mutation site. CONCLUSION This probe capture NGS assay demonstrates the potential of NIPT for β-hemoglobinopathies.
Collapse
Affiliation(s)
- Henry A Erlich
- Department of Genetics and Genomics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Christian López-Peña
- Department of Genetics and Genomics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Katie T Carlberg
- Department of Hematology/Oncology, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
| | - Shelly Shih
- Department of Genetics and Genomics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Gunmeet Bali
- Department of Genetics and Genomics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | | | | | - Reena Das
- Post Graduate Institute of Medical and Educational Research, Chandigarh, India
| | - Ashutosh Lal
- Department of Hematology/Oncology, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
| | - Cassandra D Calloway
- Department of Genetics and Genomics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
- Department of Hematology/Oncology, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
| |
Collapse
|
6
|
Non-invasive prenatal diagnosis and screening for monogenic disorders. Eur J Obstet Gynecol Reprod Biol 2020; 253:320-327. [PMID: 32907778 DOI: 10.1016/j.ejogrb.2020.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/20/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023]
Abstract
Cell-free fetal DNA (cffDNA) can be detected in the maternal circulation from 4 weeks gestation, and is present with cell-free maternal DNA at a level of between 5 % and 20 %. Cell-free DNA (cfDNA) can be extracted from a maternal blood sample and, although it is not possible to separate the fetal from the maternal cfDNA, it has enabled non-invasive prenatal diagnosis (NIPD) without the associated miscarriage risk that accompanies invasive testing. NIPD for monogenic diseases was first reported in 2000 and since then there have been many proof of principle studies showing how analysis of cfDNA can provide a definitive diagnosis early in pregnancy for a wide range of single gene diseases. Testing for a number of these diseases has been available in the UK National Health Service (NHS) since 2012. This review highlights the main techniques that are being used for NIPD and discusses the technical limitations of the methods, as well as the advances that are being made to overcome some of the issues. NIPD is technologically challenging for a number of reasons. Firstly, because it requires the detection of low level fetal variants in a high maternal background. For de novo and paternally-inherited variants this has been achieved through the use of techniques such as next-generation sequencing (NGS) and digital PCR to detect variants in the cffDNA that are not present in the maternal cfDNA. However, for maternally-inherited variants this is much more challenging and relies on dosage-based techniques to detect small differences in the levels of mutant and wild-type alleles. Alongside the technical advances that are making NIPD more widely available in both the public healthcare and commercial settings, it is crucial that we continue to monitor the social and ethical impact to ensure that patients are being offered safe and accurate testing.
Collapse
|
7
|
van Campen J, Silcock L, Yau S, Daniel Y, Ahn JW, Ogilvie C, Mann K, Oteng-Ntim E. A novel non-invasive prenatal sickle cell disease test for all at-risk pregnancies. Br J Haematol 2020; 190:119-124. [PMID: 32097993 DOI: 10.1111/bjh.16529] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/17/2020] [Indexed: 12/11/2022]
Abstract
Sickle cell disease (SCD) is the most common genetic haematological disorder. The availability of non-invasive prenatal diagnosis (NIPD) is predicted to increase uptake of prenatal diagnosis for SCD, as it has no perceived procedure-related miscarriage risk. We report the development of a targeted massively parallel sequencing (MPS) assay for the NIPD of fetal SCD using fetal cell-free (cf)DNA from maternal plasma, with no requirement for paternal or proband samples. In all, 64 plasma samples from pregnant women were analysed: 42 from SCD carriers, 15 from women with homozygous (Hb SS) SCD and seven from women with compound heterozygous (Hb SC) SCD. Our assay incorporated a relative mutation dosage assay for maternal carriers and a wild type allele detection assay for affected women (Hb SS/Hb SC). Selective analysis of only smaller cfDNA fragments and modifications to DNA fragment hybridisation capture improved diagnostic accuracy. Clinical sensitivity was 100% and clinical specificity was 100%. One sample with a fetal fraction of <4% was correctly called as 'unaffected', but with a discordant genotype (Hb AA rather than Hb AS). Six samples gave inconclusive results, of which two had a fetal fraction of <4%. This study demonstrates that NIPD for SCD is approaching clinical utility.
Collapse
Affiliation(s)
- Julia van Campen
- Genetics Laboratories, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Lee Silcock
- Nonacus Ltd., Birmingham Research Park, Birmingham, UK
| | - Shu Yau
- Viapath Genetics Laboratories, Guy's Hospital, London, UK
| | - Yvonne Daniel
- Viapath Haematological Sciences Laboratories, Guy's Hospital, London, UK
| | - Joo Wook Ahn
- Genetics Laboratories, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Caroline Ogilvie
- Genetics Laboratories, Guy's and St. Thomas' NHS Foundation Trust, London, UK.,Department of Medical and Molecular Genetics, King's College, London, UK
| | - Kathy Mann
- Viapath Genetics Laboratories, Guy's Hospital, London, UK
| | - Eugene Oteng-Ntim
- Department of Women and Children's Health, King's College, London, UK.,Department of Women's Services, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| |
Collapse
|
8
|
Chitty LS, Hui L, Ghidini A, Levy B, Deprest J, Van Mieghem T, Bianchi DW. In case you missed it: The Prenatal Diagnosis editors bring you the most significant advances of 2019. Prenat Diagn 2020; 40:287-293. [PMID: 31875323 DOI: 10.1002/pd.5632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/21/2022]
Affiliation(s)
- L S Chitty
- London North Genomic Laboratory, Great Ormond Street NHS Foundation Trust, and Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - L Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
| | - A Ghidini
- Antenatal Testing Centre, Inova Alexandria Hospital, Alexandria, VA
| | - B Levy
- Departments of Pathology and Cell Biology, Columbia University, New York, NY
| | - J Deprest
- Departments of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - T Van Mieghem
- Department of Obstetrics and Gynaecology, Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
| | - D W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| |
Collapse
|