Using massively parallel shotgun sequencing of maternal plasmatic cell-free DNA for cytomegalovirus DNA detection during pregnancy: a proof of concept study

Chesnais, Virginie; Chaplais, Emmanuel; Gabillard, Samuel; Pallares, Diego; Vauloup‐Fellous, Christelle; Benachi, Alexandra; Costa, Jean‐Marc; Ginoux, Eric

doi:10.1038/s41598-018-22414-6

Cited by 15 publications

(16 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Finally, four single case reports offer tantalizing additional evidence that measurements of cfDNA may be useful in infections and malignancies associated with viruses other than EBV and CMV. A recent study by Chesnais et al successfully detected CMV cfDNA sequences in mothers with low CMV viral loads (56) and also detected other viruses in some mothers and preterm babies. Two single case reports for Kaposi's sarcoma and BK polyomavirus-associated bladder cancer demonstrated that quantitative measurements of cfDNA containing human herpesvirus 8 or BK virus were useful in tumor detection and therapeutic monitoring of these two virus-associated cancers (57,58).…”

Section: Discussionmentioning

confidence: 99%

Does Size Matter? Comparison of Extraction Yields for Different-Sized DNA Fragments by Seven Different Routine and Four New Circulating Cell-Free Extraction Methods

et al. 2018

View full text Add to dashboard Cite

An element essential for PCR detection of microbial agents in many sample types is the extraction step, designed to purify nucleic acids. Despite the importance of this step, yields have not been extensively compared across methods to determine whether the method used contributes to quantitative differences and the lack of commutability seen with existing clinical methods. This may in part explain why plasma and blood viral load assays have proven difficult to standardize. Also, studies have identified small DNA fragments of <200 bp in plasma (cell-free DNA [cfDNA]), which may include significant quantities of viral DNA. Our study evaluated extraction yields for 11 commercially available extraction methods, including 4 new methods designed to isolate cfDNA. Solutions of DNA fragments with sizes ranging from 50 to 1,500 bp were extracted, and then the eluates were tested by droplet digital PCR to determine the DNA fragment yield for each method. The results demonstrated a wide range of extraction yields across the variety of methods/instruments used, with the 50- and 100-bp fragment sizes showing especially inconsistent quantitative results and poor yields of less than 20%. Slightly higher, more consistent yields were seen with 2 of the 4 circulating cell-free extraction kits. These results demonstrate a significant need for further evaluation of nucleic acid yields across the variety of extraction platforms and highlight the poor extraction yields of small DNA fragments by existing methods. Further work is necessary to determine the impact of this inconsistency across instruments and the relevance of the low yields for smaller DNA fragments in clinical virology testing.

show abstract

Section: Discussionmentioning

confidence: 99%

Does Size Matter? Comparison of Extraction Yields for Different-Sized DNA Fragments by Seven Different Routine and Four New Circulating Cell-Free Extraction Methods

et al. 2018

View full text Add to dashboard Cite

show abstract

“…The resulting TOM-based network was exported for visualization with Cytoscape ( 29 ). With nodes representing microorganisms identified, an edge was defined as the TOM-based similarity between any pair of two organisms.…”

Section: Methodsmentioning

confidence: 99%

Peripheral Blood Microbiome Analysis via Noninvasive Prenatal Testing Reveals the Complexity of Circulating Microbial Cell-Free DNA

Tong

et al. 2022

Microbiol Spectr

View full text Add to dashboard Cite

While circulating cell-free DNA (cfDNA) has been becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a baseline for microbial cfDNA in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Standard low-pass whole-genome-sequencing-based NIPT shares many similarities with the sequencing protocol for metagenomics and could provide a microbial cfDNA baseline in healthy people; thus, a reference cfDNA data set of the human microbiome was established with sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening.

show abstract

“…Zasad je istraživanjem potvrđena mogućnost identifikacije humanog citomegalovirusa i herpes B virusa. Ova otkrića omogućila bi pravovremenu terapiju majke hiperimunim gamaglobulinima te sprječavanje transmisije virusa kroz placentu 85 .…”

Section: Metoda Sekvenciranja Nasumičnim Pristupomunclassified

Metode molekularne dijagnostike u prenatalnoj medicini

Zaninović

Bojanac

Bašković

2022

Med. Flum. (Online)

View full text Add to dashboard Cite

Prenatalna medicina u smislu probira kromosomskih abnormalnosti fetusa nastala je 70-ih godina prošlog stoljeća. U 21. stoljeću, s razvojem tehnologija napredne i brze analize genoma, kao što su kromosomalni microarray te sekvenciranje genoma sljedeće generacije, prenatalna dijagnostika proširila se s najčešćih aneuploidija na detekciju i brojnih drugih strukturalnih kromosomskih poremećaja (povećanje broja kopija gena, delecije, duplikacije), kao i monogenskih bolesti. Osim klasičnih invazivnih tehnika (biopsija korionskih resica, amniocenteza) kojima se prikupljaju stanice za citogenetičku i genomsku analizu, danas je moguće neinvazivno analizirati genom fetusa putem analize slobodne deoksiribonukleinske kiseline (DNK) (engl. cell-free deoxyribonucleic acid) izolirane iz krvi majke. S obzirom na svoju relativno veliku točnost, jednostavnost i mogućnost rane primjene, izgledno je da će ovakvo neinvazivno testiranje zamijeniti klasični probir u prvom tromjesečju koji je kombinirao biokemijske i fetalne ultrazvučne parametre. Nema sumnje da će neinvazivni probir analizom cfDNA, uz korištenje modernih tehnologija sekvenciranja, sve više postati dijagnostički iskoristiv u prenatalnoj medicini. Ipak, problem možda leži u analizi genomskih podataka gdje se katkad detektiraju promjene u slijedu nukleotida za koje je klinička signifikantnost nepoznata i još ne postoji jasno definiran postupnik kliničkog djelovanja nakon takvih podataka. Cilj ovog preglednog rada je iz različitih izvora, kliničkih podataka, preglednih članaka te metaanaliza izložiti koherentan pregled suvremenih probirnih i dijagnostičkih molekularnih metoda u prenatalnoj medicini. Istaknute su prednosti i mane korištenja metoda probira te analitičke mogućnosti pojedinih molekularnih metoda, s krajnjim kritičkim osvrtom i konceptualizacijom budućnosti ovakvih postupaka.

show abstract

Using massively parallel shotgun sequencing of maternal plasmatic cell-free DNA for cytomegalovirus DNA detection during pregnancy: a proof of concept study

Cited by 15 publications

References 42 publications

Does Size Matter? Comparison of Extraction Yields for Different-Sized DNA Fragments by Seven Different Routine and Four New Circulating Cell-Free Extraction Methods

Does Size Matter? Comparison of Extraction Yields for Different-Sized DNA Fragments by Seven Different Routine and Four New Circulating Cell-Free Extraction Methods

Peripheral Blood Microbiome Analysis via Noninvasive Prenatal Testing Reveals the Complexity of Circulating Microbial Cell-Free DNA

Metode molekularne dijagnostike u prenatalnoj medicini

Contact Info

Product

Resources

About