Development of a comprehensive noninvasive prenatal test Article Swipe
Carolina Malcher
,
Guilherme Lopes Yamamoto
,
Philip Burnham
,
Suzana Ezquina
,
Naila Cristina Vilaça Lourenço
,
Sahilla Balkassmi
,
David Santos Marco Antônio
,
Gabriella Shih Ping Hsia
,
Thomaz Rafael Gollop
,
Rita C.M. Pavanello
,
Marco Antônio Borges Lopes
,
Egbert Bakker
,
Mayana Zatz
,
Débora Romeo Bertola
,
Iwijn De Vlaminck
,
Maria Rita Passos‐Bueno
·
YOU?
·
· 2018
· Open Access
·
· DOI: https://doi.org/10.1590/1678-4685-gmb-2017-0177
YOU?
·
· 2018
· Open Access
·
· DOI: https://doi.org/10.1590/1678-4685-gmb-2017-0177
Our aim was to develop and apply a comprehensive noninvasive prenatal test (NIPT) by using high-coverage targeted next-generation sequencing to estimate fetal fraction, determine fetal sex, and detect trisomy and monogenic disease without parental genotype information. We analyzed 45 pregnancies, 40 mock samples, and eight mother-child pairs to generate 35 simulated datasets. Fetal fraction (FF) was estimated based on analysis of the single nucleotide polymorphism (SNP) allele fraction distribution. A Z-score was calculated for trisomy of chromosome 21 (T21), and fetal sex detection. Monogenic disease detection was performed through variant analysis. Model validation was performed using the simulated datasets. The novel model to estimate FF was robust and accurate (r2= 0.994, p-value < 2.2e-16). For samples with FF > 0.04, T21 detection had 100% sensitivity (95% CI: 63.06 to 100%) and 98.53% specificity (95% CI: 92.08 to 99.96%). Fetal sex was determined with 100% accuracy. We later performed a proof of concept for monogenic disease diagnosis of 5/7 skeletal dysplasia cases. In conclusion, it is feasible to perform a comprehensive NIPT by using only data from high coverage targeted sequencing, which, in addition to detecting trisomies, also make it possible to identify pathogenic variants of the candidate genes for monogenic diseases.
Related Topics
Concepts
Trisomy
Biology
Single-nucleotide polymorphism
Fraction (chemistry)
Genetics
SNP
Allele
Prenatal diagnosis
Fetus
Genotype
Bioinformatics
Computational biology
Gene
Pregnancy
Organic chemistry
Chemistry
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1590/1678-4685-gmb-2017-0177
- http://www.scielo.br/pdf/gmb/v41n3/1415-4757-GMB-1678-4685-GMB-2017-0177.pdf
- OA Status
- gold
- Cited By
- 9
- References
- 55
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2883203449
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2883203449Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1590/1678-4685-gmb-2017-0177Digital Object Identifier
- Title
-
Development of a comprehensive noninvasive prenatal testWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2018Year of publication
- Publication date
-
2018-07-16Full publication date if available
- Authors
-
Carolina Malcher, Guilherme Lopes Yamamoto, Philip Burnham, Suzana Ezquina, Naila Cristina Vilaça Lourenço, Sahilla Balkassmi, David Santos Marco Antônio, Gabriella Shih Ping Hsia, Thomaz Rafael Gollop, Rita C.M. Pavanello, Marco Antônio Borges Lopes, Egbert Bakker, Mayana Zatz, Débora Romeo Bertola, Iwijn De Vlaminck, Maria Rita Passos‐BuenoList of authors in order
- Landing page
-
https://doi.org/10.1590/1678-4685-gmb-2017-0177Publisher landing page
- PDF URL
-
https://www.scielo.br/pdf/gmb/v41n3/1415-4757-GMB-1678-4685-GMB-2017-0177.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
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https://www.scielo.br/pdf/gmb/v41n3/1415-4757-GMB-1678-4685-GMB-2017-0177.pdfDirect OA link when available
- Concepts
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Trisomy, Biology, Single-nucleotide polymorphism, Fraction (chemistry), Genetics, SNP, Allele, Prenatal diagnosis, Fetus, Genotype, Bioinformatics, Computational biology, Gene, Pregnancy, Organic chemistry, ChemistryTop concepts (fields/topics) attached by OpenAlex
- Cited by
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9Total citation count in OpenAlex
- Citations by year (recent)
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2025: 1, 2022: 1, 2021: 2, 2020: 2, 2019: 2Per-year citation counts (last 5 years)
- References (count)
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55Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| primary_topic.display_name | Prenatal Screening and Diagnostics |
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| primary_location.raw_type | journal-article |
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| primary_location.is_accepted | True |
| primary_location.is_published | True |
| primary_location.raw_source_name | Genetics and Molecular Biology |
| primary_location.landing_page_url | https://doi.org/10.1590/1678-4685-gmb-2017-0177 |
| publication_date | 2018-07-16 |
| publication_year | 2018 |
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| abstract_inverted_index.40 | 40 |
| abstract_inverted_index.45 | 38 |
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| abstract_inverted_index.In | 161 |
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| abstract_inverted_index.5/7 | 157 |
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