Universal Haplotype-Based Noninvasive Prenatal Testing for Single Gene Diseases

Hui, Winnie W I; Jiang, Peiyong; Yu, Tong; Lee, Wing‐Shan; Cheng, Yin Cheong; New, Maria I.; Kadir, Rezan A.; Chan, Ka‐Kui; Leung, Tak Yeung; Lo, Y.M. Dennis; Chiu, Rossa W.̉K.

doi:10.1373/clinchem.2016.268375

Cited by 97 publications

(90 citation statements)

References 29 publications

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“…The discovery of circulating cell-free fetal nucleic acids in maternal plasma has enabled the development of noninvasive prenatal diagnosis of fetal aneuploidy and monogenic diseases through detection of the pathogenic mutations, allelic imbalances, and chromosomal imbalances (60,61). However, it remains difficult to study placental pathology using cell-free fetal nucleic acids.…”

Section: Discussionmentioning

confidence: 99%

Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

Tsang

Vong

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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265

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The human placenta is a dynamic and heterogeneous organ critical in the establishment of the fetomaternal interface and the maintenance of gestational well-being. It is also the major source of cell-free fetal nucleic acids in the maternal circulation. Placental dysfunction contributes to significant complications, such as preeclampsia, a potentially lethal hypertensive disorder during pregnancy. Previous studies have identified significant changes in the expression profiles of preeclamptic placentas using whole-tissue analysis. Moreover, studies have shown increased levels of targeted RNA transcripts, overall and placental contributions in maternal cell-free nucleic acids during pregnancy progression and gestational complications, but it remains infeasible to noninvasively delineate placental cellular dynamics and dysfunction at the cellular level using maternal cell-free nucleic acid analysis. In this study, we addressed this issue by first dissecting the cellular heterogeneity of the human placenta and defined individual cell-type-specific gene signatures by analyzing more than 24,000 nonmarker selected cells from full-term and early preeclamptic placentas using large-scale microfluidic single-cell transcriptomic technology. Our dataset identified diverse cellular subtypes in the human placenta and enabled reconstruction of the trophoblast differentiation trajectory. Through integrative analysis with maternal plasma cell-free RNA, we resolved the longitudinal cellular dynamics of hematopoietic and placental cells in pregnancy progression. Furthermore, we were able to noninvasively uncover the cellular dysfunction of extravillous trophoblasts in early preeclamptic placentas. Our work showed the potential of integrating transcriptomic information derived from single cells into the interpretation of cell-free plasma RNA, enabling the noninvasive elucidation of cellular dynamics in complex pathological conditions. single-cell transcriptomics | cell-free RNA | noninvasive prenatal testing | placenta | preeclampsia

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Section: Discussionmentioning

confidence: 99%

Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

Tsang

Vong

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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265

267

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“…24,25 These data, as well as those from our earlier study, show that the RHDO approach could pinpoint the site of recombination fairly precisely. 18,26 Approximately one third of all hemophilia A sequence variants occur de novo. 27 Until recently, maternal plasma DNA sequencing of de novo sequence variants faced technical limitations because of sequencing error rates of MPS platforms.…”

Section: Discussionmentioning

confidence: 99%

“…However, linked-read haplotype sequencing technology can establish mutation haplotype signature in the carrier sample directly, and thus permits PND without the availability of the proband. 26 Alternative methods for maternal haplotyping thus hold promise in resolving this issue and open up new potential targets for further refinements of NIPT-based protocols for other monogenic diseases. 26 The present developments in NIPT of hemophilia by ddPCR offer an affordable method to detect a spectrum of predefined sequence variants in the F8 and F9 genes in maternal plasma.…”

Section: Discussionmentioning

confidence: 99%

“…26 Alternative methods for maternal haplotyping thus hold promise in resolving this issue and open up new potential targets for further refinements of NIPT-based protocols for other monogenic diseases. 26 The present developments in NIPT of hemophilia by ddPCR offer an affordable method to detect a spectrum of predefined sequence variants in the F8 and F9 genes in maternal plasma. In a clinical setting, ddPCR analysis would first assess the fetal sex through chromosome Y or other paternally inherited SNP markers.…”

Section: Discussionmentioning

confidence: 99%

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Noninvasive detection of F8 int22h-related inversions and sequence variants in maternal plasma of hemophilia carriers

Hudecova

Jiang

Davies

et al. 2017

Blood

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Key Points• Droplet digital PCR is an affordable and user-friendly method for the detection of F8 and F9 sequence variants in maternal plasma.• Targeted MPS accurately determines fetal inheritance of F8 int22h-related inversions, using maternal plasma of pregnant hemophilia carriers.Direct detection of F8 and F9 sequence variants in maternal plasma of hemophilia carriers has been demonstrated by microfluidics digital PCR. Noninvasive prenatal assessment of the most clinically relevant group of sequence variants among patients with hemophilia, namely, those involving int22h-related inversions disrupting the F8 gene, poses additional challenges because of its molecular complexity. We investigated the use of droplet digital PCR (ddPCR) and targeted massively parallel sequencing (MPS) for maternal plasma DNA analysis to noninvasively determine fetal mutational status in pregnancies at risk for hemophilia. We designed family-specific ddPCR assays to detect causative sequence variants scattered across the F8 and F9 genes. A haplotype-based approach coupled with targeted MPS was applied to deduce fetal genotype by capturing a 7.6-Mb region spanning the F8 gene in carriers with int22h-related inversions. The ddPCR analysis correctly determined fetal hemophilia status in 15 at-risk pregnancies in samples obtained from 8 to 42 weeks of gestation. There were 3 unclassified samples, but no misclassification. Detailed fetal haplotype maps of the F8 gene region involving int22h-related inversions obtained through targeted MPS enabled correct diagnoses of fetal mutational status in 3 hemophilia families. Our data suggest it is feasible to apply targeted MPS to interrogate maternally inherited F8 int22h-related inversions, whereas ddPCR represents an affordable approach for the identification of F8 and F9 sequence variants in maternal plasma. These advancements may bring benefits for the pregnancy management for carriers of hemophilia sequence variants; in particular, the common F8 int22h-related inversions, associated with the most severe clinical phenotype. (Blood. 2017;130(3):340-347)

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“…In the case of 21-hydroxylase deficiency, HLA-B was genotyped after a close genetic linkage with 21-hydroxylase deficiency has been demonstrated [Levine et al, 1978]. These studies were abandoned once CYP21A2 gene analysis became available in chorionic villous samples or in amniotic fluid cells [New, 1990] and, recently, in maternal plasma cell-free fetal DNA [Hui et al, 2017].…”

Section: Discovery Of Steroid Hormones Methods For Quantification Amentioning

confidence: 99%

Development of Laboratory Investigations in Disorders of Sex Development

Audí

Camats²,

Fernández‐Cancio³

et al. 2017

Sex Dev

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Scientific knowledge to understand the biological basis of sex development was prompted by the observation of variants different from the 2 most frequent body types, and this became one of the fields first studied by modern pediatric endocrinology. The clinical observation was supported by professionals working in different areas of laboratory sciences which led to the description of adrenal and gonadal steroidogenesis, the enzymes involved, and the different deficiencies. Steroid hormone measurements evolved from colorimetry to radioimmunoassay (RIA) and automated immunoassays, although gas and liquid chromatography coupled to mass spectrometry are now the gold standard techniques for steroid measurements. Peptide hormones and growth factors were purified, and their measurement evolved from RIA to automated immunoassays. Hormone action mechanisms were described, and their specific receptors were characterized and assayed in experimental materials and in patient tissues and cell cultures. The discovery of the genetic basis for variant sex developments began with the description of the sex chromosomes. Molecular technology allowed cloning of genes coding for the different proteins involved in sex determination and development. Experimental animal models aided in verifying the roles of proteins and also suggested new genes to be investigated. New candidate genes continue to be described based on experimental models and on next-generation sequencing of patient DNAs.

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Universal Haplotype-Based Noninvasive Prenatal Testing for Single Gene Diseases

Cited by 97 publications

References 29 publications

Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

Noninvasive detection of F8 int22h-related inversions and sequence variants in maternal plasma of hemophilia carriers

Development of Laboratory Investigations in Disorders of Sex Development

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