Bayesian-based noninvasive prenatal diagnosis of single-gene disorders

Rabinowitz, Tom; Polsky, Avital; Golan, David E.; Danilevsky, Artem; Shapira, Guy; Raff, Chen; Basel‐Salmon, Lina; Matar, Reut; Shomron, Noam

doi:10.1101/gr.235796.118

Cited by 36 publications

(39 citation statements)

References 37 publications

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“…We recently presented a novel framework for genome-wide NIPD of monogenic diseases that does not rely on parental haplotype information [37] . Our approach consists of a Bayesian algorithm that utilizes characteristics that facilitate distinguishing fetal from maternal fragments, e.g.…”

Section: Methods For Genome-wide Nipd Of Monogenic Disordersmentioning

confidence: 99%

Genome-wide noninvasive prenatal diagnosis of monogenic disorders: Current and future trends

Rabinowitz

Shomron

2020

Computational and Structural Biotechnology Journal

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Section: Methods For Genome-wide Nipd Of Monogenic Disordersmentioning

confidence: 99%

Genome-wide noninvasive prenatal diagnosis of monogenic disorders: Current and future trends

Rabinowitz

Shomron

2020

Computational and Structural Biotechnology Journal

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“…In the current version of FinaleDB, we collected 2579 paired-end cfDNA WGS datasets across 23 different pathological conditions from Gene Expression Omnibus (GEO), EGA, and dbGaP, with approximately 6TB post-processed data to download ( Supplementary Table 1-2) (Snyder et al, 2016;Adalsteinsson et al, 2017;Cristiano et al, 2019;Jiang et al, 2015;Burnham et al, 2018;Rabinowitz et al, 2019;Sun et al, 2019). We processed the raw sequencing datasets by an in-house workflow (https://github.com/epifluidlab/finaledb_workflow).…”

Section: The Databasementioning

confidence: 99%

FinaleDB: a browser and database of cell-free DNA fragmentation patterns

Zheng

Zhu

Liu

2020

Preprint

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SummaryCirculating cell-free DNA (cfDNA) is a promising biomarker for the diagnosis and prognosis of many diseases, including cancer. The genome-wide non-random fragmentation patterns of cfDNA are associated with the nucleosomal protection, epigenetic environment, and gene expression in the cell types that contributed to cfDNA. However, current progress on the development of computational methods and understanding of molecular mechanisms behind cfDNA fragmentation patterns is significantly limited by the controlled-access of cfDNA whole-genome sequencing (WGS) dataset. Here, we present FinaleDB (FragmentatIoN AnaLysis of cEll-free DNA DataBase), a comprehensive database to host thousands of uniformly processed and curated de-identified cfDNA WGS datasets across different pathological conditions. Furthermore, FinaleDB comes with a fragmentation genome browser, from which users can seamlessly integrate thousands of other omics data in different cell types to experience a comprehensive view of both gene-regulatory landscape and cfDNA fragmentation patterns.Availability and implementationFinaleDB service: http://finaledb.research.cchmc.org/ FinaleDB source code: https://github.com/epifluidlab/finaledb_portal and https://github.com/epifluidlab/finaledb_workflow.Contactlyping1986@gmail.com

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“…Analysis of cfDNA for NIPT‐M would be expected to have equivalence with CVS as a diagnostic method given the placental origin of the cfDNA, whereas amniocentesis may be recommended for cases in which placental cfDNA may not reflect the fetal genotype (eg, rare autosomal trisomies identified in NIPT‐A). Although the current expense of sequencing required for RHDO methods may prohibit widespread clinical use, ongoing development of methods involving machine learning and the preferential identification of cfDNA fragments of placental origin may improve the applicability of these techniques …”

Section: What Will Be the Role Of Noninvasive Prenatal Testing As A Fmentioning

confidence: 99%

The role of prenatal diagnosis following preimplantation genetic testing for single‐gene conditions: A historical overview of evolving technologies and clinical practice

Hardy

2020

Prenatal Diagnosis

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Preimplantation genetic testing for monogenic conditions (PGT-M) has become a valued reproductive option for couples at risk of having a child with a single gene condition. In line with developments in molecular genetics, there has been an overall trend toward laboratory techniques with higher accuracy in comparison to earlier PGT-M techniques. The recommendation for confirmatory prenatal diagnostic testing has remained a standard component of PGT-M counseling, reflecting the inherent difficulties of testing the limited number of cells obtained from embryo biopsy, as well as recognition of the biological and human factors that may lead to misdiagnosis in a PGT-M cycle. Reported misdiagnosis rates are less than 1 in 200 pregnancies following PGT-M, although updated data regarding newer methods of PGT-M are required. There is limited evidence available regarding clinician and patient behavior in pregnancies resulting from PGT-M cycles. It remains essential that clinicians involved in the care of patients undergoing PGT-M provide appropriate counseling regarding the risks of misdiagnosis and the importance of confirmatory prenatal diagnosis. The nature of PGT-M test design lends itself to cell-free DNA-based noninvasive prenatal testing for monogenic conditions (NIPT-M), which is likely to become a popular method in the near future.

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Bayesian-based noninvasive prenatal diagnosis of single-gene disorders

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Cited by 36 publications

References 37 publications

Genome-wide noninvasive prenatal diagnosis of monogenic disorders: Current and future trends

Genome-wide noninvasive prenatal diagnosis of monogenic disorders: Current and future trends

FinaleDB: a browser and database of cell-free DNA fragmentation patterns

The role of prenatal diagnosis following preimplantation genetic testing for single‐gene conditions: A historical overview of evolving technologies and clinical practice

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