Cell-Free DNA in the Investigation of Miscarriage

Approximately one in four pregnancies result in pregnancy loss, and ~50% of these miscarriages are caused by chromosomal abnormalities. Genetic investigations are recommended after three consecutive miscarriages on products of conception (POC) tissue. Cell-free DNA (cfDNA) has been utilised for prenatal screening, but very little work has been carried out in nonviable pregnancies. We investigated the use of cfDNA from maternal blood to identify chromosomal abnormalities in miscarriage. One hundred and two blood samples from women experiencing a first trimester miscarriage were collected and stored. The mean gestational age was 7.1 weeks (range: 5–11 weeks). In this research, samples without a genetic test result from POC were not analysed. CfDNA was extracted and analysed using a modified commercial genome-wide non-invasive prenatal test. No results were provided to the patient. In 57 samples, cytogenetic results from POC analysis were available. Chromosomal abnormalities were identified in 47% (27/57) of POC analyses, and cfDNA analysis correctly identified 59% (16/27) of these. In total, 75% (43/57) of results were correctly identified. The average cfDNA fetal fraction was 6% (2–19%). In conclusion, cfDNA can be used to detect chromosomal abnormalities in miscarriages where the ‘fetal fraction’ is high enough; however, more studies are required to identify variables that can affect the overall results.

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Alterations of 5-hydroxymethylation in circulating cell-free DNA reflect molecular distinctions of subtypes of non-Hodgkin lymphoma

npj Genomic Medicine ◽

10.1038/s41525-021-00179-8 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Brian C.-H. Chiu ◽

Chang Chen ◽

Qiancheng You ◽

Rudyard Chiu ◽

Girish Venkataraman ◽

...

Keyword(s):

B Cell Lymphoma ◽

Cell Free Dna ◽

Invasive Approach ◽

Non Invasive ◽

Signature Genes ◽

Non Hodgkin Lymphoma ◽

Free Dna ◽

Genome Wide ◽

Circulating Cell Free Dna

AbstractThe 5-methylcytosines (5mC) have been implicated in the pathogenesis of diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). However, the role of 5-hydroxymethylcytosines (5hmC) that are generated from 5mC through active demethylation, in lymphomagenesis is unknown. We profiled genome-wide 5hmC in circulating cell-free DNA (cfDNA) from 73 newly diagnosed patients with DLBCL and FL. We identified 294 differentially modified genes between DLBCL and FL. The differential 5hmC in the DLBCL/FL-differentiating genes co-localized with enhancer marks H3K4me1 and H3K27ac. A four-gene panel (CNN2, HMG20B, ACRBP, IZUMO1) robustly represented the overall 5hmC modification pattern that distinguished FL from DLBCL with an area under curve of 88.5% in the testing set. The median 5hmC modification levels in signature genes showed potential for separating patients for risk of all-cause mortality. This study provides evidence that genome-wide 5hmC profiles in cfDNA differ between DLBCL and FL and could be exploited as a non-invasive approach.

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Modeling cell-free DNA fragment size densities for non-invasive detection of cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.3058 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 3058-3058

Author(s):

Jacob Carey ◽

Bryan Chesnick ◽

Denise Butler ◽

Michael Rongione ◽

Giovanni Parmigiani ◽

...

Keyword(s):

Fragment Size ◽

Length Distribution ◽

Mixture Component ◽

Base Pairs ◽

Machine Model ◽

Cell Free Dna ◽

Non Invasive ◽

Free Dna ◽

Genome Wide ◽

Low Coverage

3058 Background: Circulating cell-free DNA (cfDNA) is largely nucleosomal in origin with typical fragment lengths of 167 base-pairs reflecting the length of DNA wrapped around-the histone and H1 linker. Given the nucleosomal origin of cfDNA, we have previously used low coverage whole genome sequencing to evaluate DNA fragmentation profiles to sensitively and specifically detect tumor-derived DNA with altered fragment lengths or coverage. Methods: Here we evaluate the use of Bayesian finite mixtures to model the fragment length distribution and demonstrate how the parameters from these models can be useful to distinguish between individuals with and without cancer. We examined the number of cfDNA fragments by size ranging from 100-220bp and approximated the mixture component location, scale, and weight using Markov Chain Monte Carlo. The performance of the method was determined using a ten-fold, ten repeat cross-validation of Gradient Boosted Machine model using 1) our previously described genome-wide fragmentation profile approach, 2) the parameters from the mixture model and 3) a combination of approaches 1) and 2) as features. Results: In this study of 215 cancer patients and 208 cancer-free individuals, we observed cross-validated AUCs of 1) 0.94, 2) 0.95, and 3) 0.97 among the three approaches. Conclusions: Our findings indicate that parsimonious mixture models may improve detection of cancer in conjunction with fragmentation profile analyses across the genome.

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First-Trimester Contingent Screening for Trisomy 21 by Fetal Nuchal Translucency and Maternal Serum Biomarkers and Maternal Blood Cell-Free DNA Testing

Journal of Fetal Medicine ◽

10.1007/s40556-018-0177-z ◽

2018 ◽

Vol 5 (3) ◽

pp. 139-143

Author(s):

Sarang Younesi ◽

Shahram Savad ◽

Soudeh Ghafouri-Fard ◽

Mohammad Mahdi Taheri-Amin ◽

Pourandokht Saadati ◽

...

Keyword(s):

Blood Cell ◽

Trisomy 21 ◽

First Trimester ◽

Nuchal Translucency ◽

Maternal Blood ◽

Maternal Serum ◽

Serum Biomarkers ◽

Dna Testing ◽

Cell Free Dna ◽

Free Dna

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Cell-Free DNA Screening for Fetal Aneuploidy

50 Studies Every Obstetrician-Gynecologist Should Know ◽

10.1093/med/9780190947088.003.0021 ◽

2021 ◽

pp. 115-120

Author(s):

Ashley N. Battarbee ◽

Neeta L. Vora

Keyword(s):

Trisomy 21 ◽

Dna Analysis ◽

Chromosomal Abnormalities ◽

Area Under The Curve ◽

First Trimester ◽

Outcome Data ◽

Cell Free Dna ◽

High Risk Women ◽

Free Dna ◽

Trimester Screening

In a prospective, multicenter blinded study at 35 international centers, the Noninvasive Examination of Trisomy (NEXT) study evaluated the performance of cell-free DNA screening for fetal trisomy compared to standard first trimester screening with nuchal translucency and serum analytes in a routine prenatal population. Among the 15,841 women who had standard screening and cell-free DNA analysis with neonatal outcome data, there were 68 chromosomal abnormalities (1 in 236). Of these, 38 were Trisomy 21 (1 in 417). Cell-free DNA analysis had a higher area under the curve (AUC) for trisomy 21, compared to standard screening (0.999 vs. 0.958, p = 0.001). Cell-free DNA analysis also had greater sensitivity, specificity, and positive predictive value compared to standard screening for trisomy 21, 18, and 13. While cell-free DNA analysis cannot detect all chromosome abnormalities, it performed better than standard screening for detection of trisomies 21, 18, and 13 in a routine population including low- and high-risk women.

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