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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (25 October 2023) | Viewed by 31700

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Dr. Elvis Zirui Dong

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Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
Interests: clinical bioinformatics; male infertility; genome sequencing; genomic variants; structural variants; prenatal diagnosis
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Tak Yeung Leung

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Guest Editor

Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
Interests: prenatal genetic screening; diagnosis and therapy of fetal abnormalities; twin pregnancy; preterm delivery; fetal growth restriction; external cephalic version
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With rapid development of technologies (such as next-generation sequencing), current prenatal genetic testing enables early and precise diagnosis of fetal genetic defects, and provides potential options for early management for the family. However, coming along with the advancement of technologies, the number of genomic variants identified through different genetic tests is dramatically increasing; however, most of them are difficult to correlate with the phenotypic presentation(s). On the other hand, even with the most comprehensive approach, such as high read-depth genome sequencing, there is still a significant proportion of fetuses which received a negative finding. Both provide significant challenges to the laboratories, clinicians, and the families to make a decision and a proper management. In addition, the spectrums of clinically significant genomic variants in fetuses with different affected systems/organs as important references are still largely unknown. Lastly, apart from being a cost-effective method, prenatal genetic testing requires rapid turn-around time, a low amount of sample input, and the awareness of sample type.

In this Special Issue, we welcome reviews, new methods (facilitating variant identification or interpretation), databases, and original articles to address the forementioned issues of prenatal genetic testing in order to provide novel insights for the readers.

We look forward to your contributions.

Dr. Elvis Zirui Dong
Prof. Dr. Tak Yeung Leung
Guest Editors

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Keywords

prenatal genetic testing
bioinformatic analysis
genome sequencing
variant interpretation
genomic variants
variant database
fetal structural anomalies

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Published Papers (10 papers)

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11 pages, 2749 KiB

Open AccessArticle

Low-Pass Genome Sequencing-Based Detection of Paternity: Validation in Clinical Cytogenetics

by Keying Li, Yilin Zhao, Matthew Hoi Kin Chau, Ye Cao, Tak Yeung Leung, Yvonne K. Kwok, Kwong Wai Choy and Zirui Dong

Genes 2023, 14(7), 1357; https://doi.org/10.3390/genes14071357 - 27 Jun 2023

Viewed by 2008

Abstract

Submission of a non-biological parent together with a proband for genetic diagnosis would cause a misattributed parentage (MP), possibly leading to misinterpretation of the pathogenicity of genomic variants. Therefore, a rapid and cost-effective paternity/maternity test is warranted before genetic testing. Although low-pass genome sequencing (GS) has been widely used for the clinical diagnosis of germline structural variants, it is limited in paternity/maternity tests due to the inadequate read coverage for genotyping. Herein, we developed rapid paternity/maternity testing based on low-pass GS with trio-based and duo-based analytical modes provided. The optimal read-depth was determined as 1-fold per case regardless of sequencing read lengths, modes, and library construction methods by using 10 trios with confirmed genetic relationships. In addition, low-pass GS with different library construction methods and 1-fold read-depths were performed for 120 prenatal trios prospectively collected, and 1 trio was identified as non-maternity, providing a rate of MP of 0.83% (1/120). All results were further confirmed via quantitative florescent PCR. Overall, we developed a rapid, cost-effective, and sequencing platform-neutral paternity/maternity test based on low-pass GS and demonstrated the feasibility of its clinical use in confirming the parentage for genetic diagnosis. Full article

(This article belongs to the Special Issue Novel Insights into Prenatal Genetic Testing)

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9 pages, 665 KiB

Open AccessArticle

Whole-Chromosome Karyotyping of Fetal Nucleated Red Blood Cells Using the Ion Proton Sequencing Platform

by Angela N. Barrett, Zhouwei Huang, Sarah Aung, Sherry S. Y. Ho, Nur Syazana Roslan, Aniza P. Mahyuddin, Arijit Biswas and Mahesh Choolani

Genes 2022, 13(12), 2257; https://doi.org/10.3390/genes13122257 - 30 Nov 2022

Viewed by 2229

Abstract

The current gold standard for the definitive diagnosis of fetal aneuploidy uses either chorionic villus sampling (CVS) or amniocentesis, both of which are which are invasive procedures carrying a procedure-related risk of miscarriage of up to 0.1–0.2%. Non-invasive prenatal diagnosis using fetal nucleated red blood cells (FNRBCs) isolated from maternal peripheral venous blood would remove this risk of miscarriage since these cells can be isolated from the mother’s blood. We aimed to detect whole-chromosome aneuploidies from single nucleated fetal red blood cells using whole-genome amplification followed by massively parallel sequencing performed on a semiconductor sequencing platform. Twenty-six single cells were picked from the placental villi of twelve patients thought to have a normal fetal genotype and who were undergoing elective first-trimester surgical termination of pregnancy. Following karyotyping, it was subsequently found that two of these cases were also abnormal (one trisomy 15 and one mosaic genotype). One single cell from chorionic villus samples for two patients carrying a fetus with trisomy 21 and two single cells from women carrying fetuses with T18 were also picked. Pooled libraries were sequenced on the Ion Proton and data were analysed using Ion Reporter software. We correctly classified fetal genotype in all 24 normal cells, as well as the 2 T21 cells, the 2 T18 cells, and the two T15 cells. The two cells picked from the fetus with a mosaic result by CVS were classified as unaffected, suggesting that this was a case of confined placental mosaicism. Fetal sex was correctly assigned in all cases. We demonstrated that semiconductor sequencing using commercially available software for data analysis can be achieved for the non-invasive prenatal diagnosis of whole-chromosome aneuploidy with 100% accuracy. Full article

(This article belongs to the Special Issue Novel Insights into Prenatal Genetic Testing)

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9 pages, 887 KiB

Open AccessArticle

An Investigation of the Etiologies of Non-Immune Hydrops Fetalis in the Era of Next-Generation Sequence—A Single Center Experience

by Xing Wei, Yingjun Yang, Jia Zhou, Xinyao Zhou, Shiyi Xiong, Jianping Chen, Fenhe Zhou, Gang Zou and Luming Sun

Genes 2022, 13(12), 2231; https://doi.org/10.3390/genes13122231 - 28 Nov 2022

Cited by 3 | Viewed by 3496

Abstract

(1) Background: Numerous etiologies may lead to non-immune hydrops fetalis (NIHF). However, the causes remain unclear in half of NIHF cases following current standard assessment. The application of prenatal chromosomal microarray analysis (CMA) and exome sequencing (ES) can improve the identification of the etiologies. This study aimed to investigate the etiologies of NIHF in the era of next-generation sequence (NGS) following a unified prenatal work-up flow for diagnosis. (2) Methods: A retrospective analysis was conducted on NIHF cases that were collected prospectively to explore the underlying etiologies according to a unified prenatal diagnosis work-up flow at Shanghai First Maternity and Infant Hospital between Jan 2016 and Dec 2019. The medical records for all NIHF cases were reviewed, and the causes of NIHF were classified as confirmed (diagnostic), suspected, or unknown. (3) Results: Prenatal and postnatal medical records for a total of 145 NIHF cases were reviewed, 48.3% (70/145) of the cases were identified to be with confirmed etiologies, and 10.3% (15/145) with suspected etiologies. Among 85 cases with confirmed or suspected etiologies, 44.7% were diagnosed with genetic disorders, 20% with chylothorax/chyloascites diagnosed postnatally, 12.9% with fetal structural anomalies, 12.9% with fetal anemia, 7% (6 cases) with fetal arrhythmia, and 2.3% (2 cases) with placenta chorioangioma. In cases with genetic disorders, 8 aneuploidies were detected by CMA, and 30 cases had single-gene disorders identified by ES (29/30) or targeted gene panel (1/30). There were still 41.4% cases (60/145) with unknown causes after this unified prenatal diagnostic work-up flow. (4) Conclusions: In the era of NGS, the causes of NIHF were identified in 58.6% of cases, with genetic disorders being the most common ones. NGS is helpful in determining the genetic etiology of NIHF when CMA results cannot explain NIHF, but 41.4% of cases were still with unknown causes under the unified prenatal diagnostic work-up flow in this single-center study. Full article

(This article belongs to the Special Issue Novel Insights into Prenatal Genetic Testing)

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26 pages, 535 KiB

Open AccessArticle

Implementation of Public Funded Genome Sequencing in Evaluation of Fetal Structural Anomalies

by Po Lam So, Annie Shuk Yi Hui, Teresa Wei Ling Ma, Wendy Shu, Amelia Pui Wah Hui, Choi Wah Kong, Tsz Kin Lo, Amanda Nim Chi Kan, Elaine Yee Ling Kan, Shuk Ching Chong, Brian Hon Yin Chung, Ho Ming Luk, Kwong Wai Choy, Anita Sik Yau Kan and Wing Cheong Leung

Genes 2022, 13(11), 2088; https://doi.org/10.3390/genes13112088 - 10 Nov 2022

Cited by 7 | Viewed by 2403

Abstract

With the advancements in prenatal diagnostics, genome sequencing is now incorporated into clinical use to maximize the diagnostic yield following uninformative conventional tests (karyotype and chromosomal microarray analysis). Hong Kong started publicly funded prenatal genomic sequencing as a sequential test in the investigation of fetal structural anomalies in April 2021. The objective of the study was to evaluate the clinical performance and usefulness of this new service over one year. We established a web-based multidisciplinary team to facilitate case selection among the expert members. We retrospectively analyzed the fetal phenotypes, test results, turnaround time and clinical impact in the first 15 whole exome sequencing and 14 whole genome sequencing. Overall, the molecular diagnostic rate was 37.9% (11/29). De novo autosomal dominant disorders accounted for 72.7% (8/11), inherited autosomal recessive disorders for 18.2% (2/11), and inherited X-linked disorders for 9.1% (1/11). The median turnaround time for ongoing pregnancy was 19.5 days (range, 13–31 days). Our study showed an overall clinical impact of 55.2% (16/29), which influenced reproductive decision-making in four cases, guided perinatal management in two cases and helped future family planning in ten cases. In conclusion, our findings support the important role of genome sequencing services in the prenatal diagnosis of fetal structural anomalies in a population setting. It is important to adopt a multidisciplinary team approach to support the comprehensive genetic service. Full article

(This article belongs to the Special Issue Novel Insights into Prenatal Genetic Testing)

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16 pages, 1135 KiB

Open AccessArticle

Prenatal Genetic Testing in the Era of Next Generation Sequencing: A One-Center Canadian Experience

by Asra Almubarak, Dan Zhang, Mackenzie Kosak, Sarah Rathwell, Jasmine Doonanco, Alison J. Eaton, Peter Kannu, Joanna Lazier, Monique Lui, Karen Y. Niederhoffer, Melissa J. MacPherson, Melissa Sorsdahl and Oana Caluseriu

Genes 2022, 13(11), 2019; https://doi.org/10.3390/genes13112019 - 3 Nov 2022

Cited by 1 | Viewed by 2703

Abstract

The introduction of next generation sequencing (NGS) technologies has revolutionized the practice of Medical Genetics, and despite initial reticence in its application to prenatal genetics (PG), it is becoming gradually routine, subject to availability. Guidance for the clinical implementation of NGS in PG, in particular whole exome sequencing (ES), has been provided by several professional societies with multiple clinical studies quoting a wide range of testing yields. ES was introduced in our tertiary care center in 2017; however, its use in relation to prenatally assessed cases has been limited to the postnatal period. In this study, we review our approach to prenatal testing including the use of microarray (CMA), and NGS technology (gene panels, ES) over a period of three years. The overall diagnostic yield was 30.4%, with 43.2% of those diagnoses being obtained through CMA, and the majority by using NGS technology (42% through gene panels and 16.6% by ES testing, respectively). Of these, 43.4% of the diagnoses were obtained during ongoing pregnancies. Seventy percent of the abnormal pregnancies tested went undiagnosed. We are providing a contemporary, one tertiary care center retrospective view of a real-life PG practice in the context of an evolving use of NGS within a Canadian public health care system that may apply to many similar jurisdictions around the world. Full article

(This article belongs to the Special Issue Novel Insights into Prenatal Genetic Testing)

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18 pages, 282 KiB

Open AccessArticle

Implementation of Exome Sequencing in Prenatal Diagnosis and Impact on Genetic Counseling: The Polish Experience

by Anna Kucińska-Chahwan, Maciej Geremek, Tomasz Roszkowski, Julia Bijok, Diana Massalska, Michał Ciebiera, Hildeberto Correia, Iris Pereira-Caetano, Ana Barreta, Ewa Obersztyn, Anna Kutkowska-Kaźmierczak, Paweł Własienko, Małgorzata Krajewska-Walasek, Piotr Węgrzyn, Lech Dudarewicz, Waldemar Krzeszowski, Magda Rybak-Krzyszkowska and Beata Nowakowska

Genes 2022, 13(5), 724; https://doi.org/10.3390/genes13050724 - 21 Apr 2022

Cited by 9 | Viewed by 2961

Abstract

Background: Despite advances in routine prenatal cytogenetic testing, most anomalous fetuses remain without a genetic diagnosis. Exome sequencing (ES) is a molecular technique that identifies sequence variants across protein-coding regions and is now increasingly used in clinical practice. Fetal phenotypes differ from postnatal and, therefore, prenatal ES interpretation requires a large amount of data deriving from prenatal testing. The aim of our study was to present initial results of the implementation of ES to prenatal diagnosis in Polish patients and to discuss its possible clinical impact on genetic counseling. Methods: In this study we performed a retrospective review of all fetal samples referred to our laboratory for ES from cooperating centers between January 2017 and June 2021. Results: During the study period 122 fetuses were subjected to ES at our institution. There were 52 abnormal ES results: 31 in the group of fetuses with a single organ system anomaly and 21 in the group of fetuses with multisystem anomalies. The difference between groups was not statistically significant. There were 57 different pathogenic or likely pathogenic variants reported in 33 different genes. The most common were missense variants. In 17 cases the molecular diagnosis had an actual clinical impact on subsequent pregnancies or other family members. Conclusions: Exome sequencing increases the detection rate in fetuses with structural anomalies and improves genetic counseling for both the affected couple and their relatives. Full article

(This article belongs to the Special Issue Novel Insights into Prenatal Genetic Testing)

12 pages, 4214 KiB

Open AccessArticle

Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception

by Nikhil Shri Sahajpal, Ashis K. Mondal, Sudha Ananth, Chetan Pundkar, Kimya Jones, Colin Williams, Timothy Fee, Amanda Weissman, Giuseppe Tripodi, Eesha Oza, Larisa Gavrilova-Jordan, Nivin Omar, Alex R. Hastie, Barbara R. DuPont, Lawrence Layman, Alka Chaubey and Ravindra Kolhe

Genes 2022, 13(4), 643; https://doi.org/10.3390/genes13040643 - 3 Apr 2022

Cited by 3 | Viewed by 3263

Abstract

Conventional cytogenetic analysis of products of conception (POC) is of limited utility because of failed cultures, as well as microbial and maternal cell contamination (MCC). Optical genome mapping (OGM) is an emerging technology that has the potential to replace conventional cytogenetic methods. The use of OGM precludes the requirement for culturing (and related microbial contamination). However, a high percentage of MCC impedes a definitive diagnosis, which can be addressed by an additional pre-analytical quality control step that includes histological assessment of H&E stained slides from formalin-fixed paraffin embedded (FFPE) tissue with macro-dissection for chorionic villi to enrich fetal tissue component for single nucleotide polymorphism microarray (SNPM) analysis. To improve the diagnostic yield, an integrated workflow was devised that included MCC characterization of POC tissue, followed by OGM for MCC-negative cases or SNPM with histological assessment for MCC-positive cases. A result was obtained in 93% (29/31) of cases with a diagnostic yield of 45.1% (14/31) with the proposed workflow, compared to 9.6% (3/31) and 6.4% (2/31) with routine workflow, respectively. The integrated workflow with these technologies demonstrates the clinical utility and higher diagnostic yield in evaluating POC specimens. Full article

(This article belongs to the Special Issue Novel Insights into Prenatal Genetic Testing)

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14 pages, 508 KiB

Open AccessReview

Next Generation Sequencing after Invasive Prenatal Testing in Fetuses with Congenital Malformations: Prenatal or Neonatal Investigation

by Alexandra Emms, James Castleman, Stephanie Allen, Denise Williams, Esther Kinning and Mark Kilby

Genes 2022, 13(9), 1517; https://doi.org/10.3390/genes13091517 - 24 Aug 2022

Cited by 13 | Viewed by 3927

Abstract

Congenital malformations diagnosed by ultrasound screening complicate 3–5% of pregnancies and many of these have an underlying genetic cause. Approximately 40% of prenatally diagnosed fetal malformations are associated with aneuploidy or copy number variants, detected by conventional karyotyping, QF-PCR and microarray techniques, however monogenic disorders are not diagnosed by these tests. Next generation sequencing as a secondary prenatal genetic test offers additional diagnostic yield for congenital abnormalities deemed to be potentially associated with an underlying genetic aetiology, as demonstrated by two large cohorts: the ‘Prenatal assessment of genomes and exomes’ (PAGE) study and ‘Whole-exome sequencing in the evaluation of fetal structural anomalies: a prospective cohort study’ performed at Columbia University in the US. These were large and prospective studies but relatively ‘unselected’ congenital malformations, with little Clinical Genetics input to the pre-test selection process. This review focuses on the incremental yield of next generation sequencing in single system congenital malformations, using evidence from the PAGE, Columbia and subsequent cohorts, with particularly high yields in those fetuses with cardiac and neurological anomalies, large nuchal translucency and non-immune fetal hydrops (of unknown aetiology). The total additional yield gained by exome sequencing in congenital heart disease was 12.7%, for neurological malformations 13.8%, 13.1% in increased nuchal translucency and 29% in non-immune fetal hydrops. This demonstrates significant incremental yield with exome sequencing in single-system anomalies and supports next generation sequencing as a secondary genetic test in routine clinical care of fetuses with congenital abnormalities. Full article

(This article belongs to the Special Issue Novel Insights into Prenatal Genetic Testing)

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11 pages, 977 KiB

Open AccessSystematic Review

Diagnostic Yield of Exome Sequencing in Fetuses with Sonographic Features of Skeletal Dysplasias but Normal Karyotype or Chromosomal Microarray Analysis: A Systematic Review

by Kai Yeung Tse, Ilham Utama Surya, Rima Irwinda, Kwok Yin Leung, Yuen Ha Ting, Ye Cao and Kwong Wai Choy

Genes 2023, 14(6), 1203; https://doi.org/10.3390/genes14061203 - 30 May 2023

Cited by 3 | Viewed by 2834

Abstract

Skeletal dysplasias are a group of diseases characterized by bone and joint abnormalities, which can be detected during prenatal ultrasound. Next-generation sequencing has rapidly revolutionized molecular diagnostic approaches in fetuses with structural anomalies. This review studies the additional diagnostic yield of prenatal exome sequencing in fetuses with prenatal sonographic features of skeletal dysplasias. This was a systematic review by searching PubMed for studies published between 2013 and July 2022 that identified the diagnostic yield of exome sequencing after normal karyotype or chromosomal microarray analysis (CMA) for cases with suspected fetal skeletal dysplasias based on prenatal ultrasound. We identified 10 out of 85 studies representing 226 fetuses. The pooled additional diagnostic yield was 69.0%. The majority of the molecular diagnoses involved de novo variants (72%), while 8.7% of cases were due to inherited variants. The incremental diagnostic yield of exome sequencing over CMA was 67.4% for isolated short long bones and 77.2% for non-isolated cases. Among phenotypic subgroup analyses, features with the highest additional diagnostic yield were an abnormal skull (83.3%) and a small chest (82.5%). Prenatal exome sequencing should be considered for cases with suspected fetal skeletal dysplasias with or without a negative karyotype or CMA results. Certain sonographic features, including an abnormal skull and small chest, may indicate a potentially higher diagnostic yield. Full article

(This article belongs to the Special Issue Novel Insights into Prenatal Genetic Testing)

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11 pages, 5967 KiB

Open AccessCase Report

Agnathia-Otocephaly Complex Due to a De Novo Deletion in the OTX2 Gene

by Marco Fabiani, Francesco Libotte, Katia Margiotti, Dina Khader Issa Tannous, Davide Sparacino, Maria Pia D’Aleo, Francesca Monaco, Claudio Dello Russo, Alvaro Mesoraca and Claudio Giorlandino

Genes 2022, 13(12), 2269; https://doi.org/10.3390/genes13122269 - 2 Dec 2022

Cited by 1 | Viewed by 4640

Abstract

Agnathia-otocephaly complex (AOC) is a rare and usually lethal malformation typically characterized by hypoplasia or the absence of the mandible, ventromedial and caudal displacement of the ears with or without the fusion of the ears, a small oral aperture with or without a tongue hypoplasia. Its incidence is reported as 1 in 70,000 births and its etiology has been attributed to both genetic and teratogenic causes. AOC is characterized by a wide severity clinical spectrum even when occurring within the same family, ranging from a mild mandibular defect to an extreme facial aberration incompatible with life. Most AOC cases are due to a de novo sporadic mutation. Given the genetic heterogeneity, many genes have been reported to be implicated in this disease but to date, the link to only two genes has been confirmed in the development of this complex: the orthodenticle homeobox 2 (OTX2) gene and the paired related homeobox 1 (PRRX1) gene. In this article, we report a case of a fetus with severe AOC, diagnosed in routine ultrasound scan in the first trimester of pregnancy. The genetic analysis showed a novel 10 bp deletion mutation c.766_775delTTGGGTTTTA in the OTX2 gene, which has never been reported before, together with a missense variant c.778T>C in cis conformation. Full article

(This article belongs to the Special Issue Novel Insights into Prenatal Genetic Testing)

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