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Hammer C, Pierson S, Acevedo A, Goldberg J, Westover T, Chawla D, Mabey B, Muzzey D, Johansen Taber K. High positive predictive value 22q11.2 microdeletion screening by prenatal cell-free DNA testing that incorporates fetal fraction amplification. Prenat Diagn 2024; 44:925-935. [PMID: 38622914 DOI: 10.1002/pd.6562] [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: 11/21/2023] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 04/17/2024]
Abstract
OBJECTIVE 22q11.2 deletion syndrome (DS) is a serious condition with a range of features. The small microdeletion causing 22q11.2DS makes it technically challenging to detect using standard prenatal cfDNA screening. Here, we assess 22q11.2 microdeletion clinical performance by a prenatal cfDNA screen that incorporates fetal fraction (FF) amplification. METHODS The study cohort consisted of patients who received Prequel (Myriad Genetics, Inc.), a prenatal cfDNA screening that incorporates FF amplification, and met additional eligibility criteria. Pregnancy outcomes were obtained via a routine process for continuous quality improvement. Samples with diagnostic testing results were used to calculate positive predictive value (PPV). RESULTS 379,428 patients met study eligibility criteria, 76 of whom were screen-positive for a de novo 22q11.2 microdeletion. 22 (29.7%) had diagnostic testing results available, and all 22 cases were confirmed as true positives, for a PPV of 100% (95% CI 84.6%-100%). This performance was based on cases that ranged broadly across FF (5.9%-41.1%, mean 23.0%), body mass index (22.3-44.8, mean 29.9), and gestational age at testing (10.0w-34.6w, median 12.7w). Ultrasound findings in screen-positive pregnancies were consistent with those known to be associated with 22q11.2DS. CONCLUSION 22q11.2 microdeletion screening that incorporates FF amplification demonstrated high PPV across both general and high-risk population cohorts.
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Affiliation(s)
- Carly Hammer
- Department of Research & Development, Myriad Genetics, Inc, South San Francisco, California, USA
| | - Summer Pierson
- Department of Research & Development, Myriad Genetics, Inc, South San Francisco, California, USA
| | - Ashley Acevedo
- Department of Research & Development, Myriad Genetics, Inc, South San Francisco, California, USA
| | - James Goldberg
- Independent (unaffiliated), Washington, District of Columbia, USA
| | - Thomas Westover
- Maternal Fetal Medicine and Perinatal Genetics, Capital Health, Trenton, New Jersey, USA
| | - Devika Chawla
- Department of Research & Development, Myriad Genetics, Inc, South San Francisco, California, USA
| | - Brent Mabey
- Department of Research & Development, Myriad Genetics, Inc, South San Francisco, California, USA
| | - Dale Muzzey
- Department of Research & Development, Myriad Genetics, Inc, South San Francisco, California, USA
| | - Katherine Johansen Taber
- Department of Research & Development, Myriad Genetics, Inc, South San Francisco, California, USA
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Doughty ES, Post MD. Fetal and Neonatal Autopsy in the Molecular Age: Exploring Tissue Selection for Testing Success. Pediatr Dev Pathol 2024; 27:148-155. [PMID: 38098260 DOI: 10.1177/10935266231214880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
While conventional autopsy is the gold-standard for determining cause of demise in the fetal and neonatal population, molecular analysis is increasingly used as an ancillary tool. Testing methods and tissue selection should be optimized to provide informative genetic results. This institutional review compares testing modalities and postmortem tissue type in 53 demises occurring between 20 weeks of gestation and 28 days of life. Testing success, defined as completion of analysis, varies by technique and may require viable cells for culture or extractable nucleic acid. Success was achieved by microarray in 29/30 tests (96.7%), karyotype in 40/54 tests (74.1%), fluorescent in situ hybridization in 5/9 tests (55.6%), and focused gene panels in 2/2 tests (100%). With respect to tissue type, postmortem prepartum amniotic fluid was analyzed to completion in 100% of tests performed; compared to 84.0%, 54.5%, and 80.8% of tests using placenta, fetal only, and mixed fetal-placental tissue collection, respectively. Sampling skin (83.3%, in cases with minimal maceration) and kidney (75.0%) were often successful, compared to lower efficacy of umbilical cord (57.1%) and liver (25.0%). Addition of genetic testing into cases with anomalous clinical and gross findings can increase the utility of the final report for family counseling and future pregnancy planning.
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Affiliation(s)
- Elizabeth S Doughty
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Miriam D Post
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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Van Dooren M, De Croon R, Swillen A, Verbert K. Bridging the Communication Gap Between People With Cognitive Impairments and Their Caregivers Using mHealth Apps: User-Centered Design and Evaluation Study With People With 22q11 Deletion Syndrome. JMIR Hum Factors 2023; 10:e44290. [PMID: 37585257 PMCID: PMC10468703 DOI: 10.2196/44290] [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: 11/28/2022] [Revised: 05/26/2023] [Accepted: 06/07/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND In families with children with cognitive impairments, both parents and children experience tension and have questions because of a lack of communication and adequate information. Therefore, there is a great need to develop tools that can help bridge the communication gap between patients and caregivers by stimulating conversations and providing psychoeducational tools. mHealth apps show great potential in this context. OBJECTIVE The objective of this research is to discover the specific ways young people with cognitive impairments and their families interact with mHealth apps in the context of bridging the communication gap. This newly discovered information leads to potentially more impactful mHealth interventions in the future. Therefore, this paper documents the design and development of a mHealth app for a specific group of people with cognitive impairments-people with 22q11 deletion syndrome (22q11 DS)-and their caregivers, as well as key learnings from the evaluation of this app. METHODS An iterative, user-centered design approach is used to design and develop the app. Design and evaluation happens in 2 phases. During the design phase, feedback is gathered from 2 medical experts and 3 human computer interaction (HCI) experts using a low-fidelity paper prototype. During the evaluation phase, feedback is gathered from 8 families with a child with 22q11 DS using a fully working proof of concept. This phase consists of a semistructured interview, a 2-4-week trial period, and a concluding semistructured interview. RESULTS The evaluation results of the fully working proof of concept led to design recommendations related to four different topics: (1) overcoming usage barriers, (2) stimulating conversation through a mHealth app, (3) providing information, and (4) bringing continual added value. Results are presented according to six different categories obtained in a thematic analysis: (1) feedback about the app "as is," (2) difficulties, (3) comparison between physical and digital tool, (4) extensions, (5) intention, and (6) other. CONCLUSIONS In this research, the need for apps that help bridge the communication gap between a person with cognitive impairment and their caregiver is confirmed. All participating families express their gratitude and mention the added value for other families. Therefore, it is highly encouraged for clinics and institutions to take action and develop an app to be used in practice. Furthermore, considerations when developing for people with 22q11 DS, or more broadly, people with cognitive impairments, are proposed. First, one should keep design principles in mind to overcome usage barriers. Next, recognition is a key concept when stimulating conversations through mobile apps. Third, information should be provided by a trusted source, and more than just clinical information can be considered valuable. Finally, having the possibility of using a digital tool that can be personalized brings continual added value.
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Affiliation(s)
| | - Robin De Croon
- Department of Computer Science, KU Leuven, Leuven, Belgium
| | - Ann Swillen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospital Gasthuisberg Leuven, Leuven, Belgium
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Lewis C, Hammond J, Klapwijk JE, Harding E, Lou S, Vogel I, Szepe EJ, Hui L, Ingvoldstad-Malmgren C, Soller MJ, Ormond KE, Choolani M, Hill M, Riedijk S. Dealing with uncertain results from chromosomal microarray and exome sequencing in the prenatal setting: An international cross-sectional study with healthcare professionals. Prenat Diagn 2021; 41:720-732. [PMID: 33724493 PMCID: PMC8519283 DOI: 10.1002/pd.5932] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/26/2021] [Indexed: 12/20/2022]
Abstract
Objectives To conduct qualitative interviews with healthcare providers working in different countries to understand their experiences of dealing with uncertain results from prenatal chromosome microarray analysis (CMA) and exome sequencing (ES). Methods Semi‐structured interviews with 31 healthcare providers who report or return prenatal CMA and/or ES results (clinicians, genetic counsellors and clinical scientists) in six countries with differing healthcare systems; Australia (4), Denmark (5), Netherlands (6), Singapore (4), Sweden (6) and United Kingdom (6). The topic guide explored the main sources of uncertainty and their management. Results There was variation in reporting practices both between and across countries for variants of uncertain significance, however, there was broad agreement on reporting practices for incidental findings. There was also variation in who decides what results are reported (clinical scientists or clinicians). Technical limitations and lack of knowledge (to classify variants and of prenatal phenotypes) were significant challenges, as were turnaround times and lack of guidelines. Conclusion Health professionals around the globe are dealing with similar sources of uncertainty, but managing them in different ways, Continued dialogue with international colleagues on ways of managing uncertain results is important to compare and contrast the benefits and limitations of the different approaches.
What's already known about this topic?
Chromosome microarray analysis and exome sequencing have increased diagnostic yield over karyotyping but have increased the incidence of uncertain results.
What does this study add?
Our findings highlight variation in reporting practices both between and across countries for variants of uncertain significance, although there is broad agreement on reporting practices for incidental findings. International guidelines may help to standardise how we define and categorise variants, however, global uniformity on the management of uncertain results may not be a realistic or desirable goal.
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Affiliation(s)
- Celine Lewis
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, London, UK.,North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, UK
| | - Jennifer Hammond
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | | | - Eleanor Harding
- BSc Paediatrics and Child Health, The UCL Great Ormond Street Institute of Child Health, London, UK
| | - Stina Lou
- Center for Fetal Diagnostics, Aarhus University Hospital, Aarhus, Denmark
| | - Ida Vogel
- Center for Fetal Diagnostics, Aarhus University Hospital, Aarhus, Denmark
| | - Emma J Szepe
- Reproductive Epidemiology, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia.,Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, Victoria, Australia.,Department of Obstetrics and Gynaecology, Northern Health, Epping, Victoria, Australia
| | - Charlotta Ingvoldstad-Malmgren
- Center for Fetal Medicine, Karolinska University Hospital, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska Hospital and Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Maria J Soller
- Department of Clinical Genetics, Karolinska Hospital and Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kelly E Ormond
- Department of Genetics and Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, California, USA
| | - Mahesh Choolani
- Department of Obstetrics & Gynaecology, National University Hospital, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Melissa Hill
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sam Riedijk
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
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Hao M, Li L, Zhang H, Li L, Liu R, Yu Y. The difference between karyotype analysis and chromosome microarray for mosaicism of aneuploid chromosomes in prenatal diagnosis. J Clin Lab Anal 2020; 34:e23514. [PMID: 32864771 PMCID: PMC7755766 DOI: 10.1002/jcla.23514] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVE To compare karyotype and chromosomal microarray (CMA) analysis of aneuploid chromosome mosaicism in amniocentesis samples. MATERIALS AND METHODS A total of 2091 amniocentesis samples from pregnant women were collected from March 1, 2019, to January 31, 2020. Karyotype analysis was performed using G-banding and CMA analysis used the Affymetrix CytoScan 750K SNP microarray. RESULT Thirteen cases with aneuploid chromosome mosaicism were detected and compared between the karyotype and CMA methods. Seven of these cases were trisomic mosaicism, and the levels of mosaicism calculated from CMA were higher than those detected from karyotype analysis; noting three cases of trisomy mosaicism were not detected by karyotype analysis. Four cases exhibited monomeric mosaicism, and the levels of mosaicism detected in three of these cases were higher in karyotype compared with CMA analysis; one case had equivalent levels of monomeric mosaicism from both karyotype and CMA analysis. Two other cases from karyotype analysis were a mix of monosomic and trisomic mosaicism, whereas the CMA result was restricted to monosomic mosaicism for these cases. CONCLUSION Both karyotype and CMA analysis can be used to detect aneuploid chromosome mosaicism. However, the two methods produced different results. CMA and karyotype analysis have their own advantages in detecting aneuploid mosaicism, and the combination of these methods provides a more rigorous diagnosis.
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Affiliation(s)
- MengZhe Hao
- Center for Reproductive MedicineCenter for Prenatal DiagnosisThe First Hospital of Jilin UniversityChangchunChina
| | - LeiLei Li
- Center for Reproductive MedicineCenter for Prenatal DiagnosisThe First Hospital of Jilin UniversityChangchunChina
| | - Han Zhang
- Center for Reproductive MedicineCenter for Prenatal DiagnosisThe First Hospital of Jilin UniversityChangchunChina
| | - LinLin Li
- Center for Reproductive MedicineCenter for Prenatal DiagnosisThe First Hospital of Jilin UniversityChangchunChina
| | - Ruizhi Liu
- Center for Reproductive MedicineCenter for Prenatal DiagnosisThe First Hospital of Jilin UniversityChangchunChina
| | - Yang Yu
- Center for Reproductive MedicineCenter for Prenatal DiagnosisThe First Hospital of Jilin UniversityChangchunChina
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