OC28.06: Potential role and clinical impact of noninvasive prenatal testing by massively parallel DNA sequencing of maternal blood

BACKGROUND Massively parallel DNA sequencing of cell-free fetal DNA from maternal blood can detect fetal chromosomal abnormalities. Although existing algorithms focus on the detection of fetal trisomy 21 (T21), these same algorithms have difficulty detecting trisomy 18 (T18). METHODS Blood samples were collected from 1014 patients at 13 US clinic locations before they underwent an invasive prenatal procedure. All samples were processed to plasma, and the DNA extracted from 119 samples underwent massively parallel DNA sequencing. Fifty-three sequenced samples came from women with an abnormal fetal karyotype. To minimize the intra- and interrun sequencing variation, we developed an optimized algorithm by using normalized chromosome values (NCVs) from the sequencing data on a training set of 71 samples with 26 abnormal karyotypes. The classification process was then evaluated on an independent test set of 48 samples with 27 abnormal karyotypes. RESULTS Mapped sites for chromosomes of interest in the sequencing data from the training set were normalized individually by calculating the ratio of the number of sites on the specified chromosome to the number of sites observed on an optimized normalizing chromosome (or chromosome set). Threshold values for trisomy or sex chromosome classification were then established for all chromosomes of interest, and a classification schema was defined. Sequencing of the independent test set led to 100% correct classification of T21 (13 of 13) and T18 (8 of 8) samples. Other chromosomal abnormalities were also identified. CONCLUSION Massively parallel sequencing is capable of detecting multiple fetal chromosomal abnormalities from maternal plasma when an optimized algorithm is used.

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Performance of Cell-Free DNA Sequencing-Based Non-invasive Prenatal Testing: Our Experience on 36456 both Singleton and Multiple Pregnancies.

10.21203/rs.3.rs-144192/v1 ◽

2021 ◽

Author(s):

Marco La Verde ◽

Luigia De Falco ◽

Annalaura Torella ◽

Giovanni Savarese ◽

Pasquale Saverese ◽

...

Keyword(s):

Dna Sequencing ◽

Retrospective Analysis ◽

False Negative ◽

Screening Method ◽

Prenatal Testing ◽

Maternal Blood ◽

Noninvasive Prenatal Testing ◽

Cell Free Dna ◽

Detection Rates ◽

Free Dna

Abstract Background: To describe the clinical practice and performance of cell-free DNA sequencing-based noninvasive prenatal testing as a screening method for detecting trisomy 21, 18, and 13 (T21, T18, and T13, respectively), as well as sex chromosome aneuploidy (SCA), in a general Italian pregnancy population.Methods: The AMES-accredited laboratory offers noninvasive prenatal testing in maternal blood as a clinical screening test for foetal T21, T18, T13 and SCA. Samples were sequenced on a NextSeq 550 (Illumina) using the VeriSeq NIPT Solution v1 assay.Results: A retrospective analysis was performed on a cohort of 36456 consecutive maternal blood samples, including 35650 singleton pregnancies, 800 twin pregnancies, and 6 triplet pregnancies, which were tested between April 2017 and September 2019. The cohort included 46% elevated-risk and 54% low-risk patients. Genetic and/or clinical outcomes were available in 36000 cases (98.7%). In the overall cohort, 356 (1%) results were indicative of classic trisomy: 254 T21, 69 T18, and 33 T13. In addition, 145 results (0.4%) were indicative of SCA. Of the combined 501 screen-positive cases, 484 had confirmatory diagnostic testing results available: 99.2% (247/249) of T21 cases, 91.2% (62/68) of T18 cases, 84.4% (27/32) of T13 cases, and 86.7% (117/135) of SCA cases were confirmed. Follow-up data were available for 98.8% of the 35955 cases reported as unaffected by trisomy or SCA. No false negative cases were reported. The sensitivity of NIPT was 100.00% for T21 (95% Cl 98.47-100.0), T18 (95% Cl 94.17-100.0), T13 (95% Cl 87.54-100.0) and SCA (95% Cl 96.62-100.0). The specificities were 99.99% (95% Cl 99.98-100.0), 99.98% (95% Cl 99.96-100.0), 99.99% (95% Cl 99.97-100.0), and 99.95% (95% Cl 99.92-99.97) for T21, T18, T13, and SCA, respectively.Conclusion: This retrospective analysis of a large cohort of consecutive patients who had whole-genome sequencing-based NIPT for classic trisomies and SCA showed excellent detection rates and low false positive rates.

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Reliable noninvasive prenatal testing by massively parallel sequencing of circulating cell-free DNA from maternal plasma processed up to 24h after venipuncture

Clinical Biochemistry ◽

10.1016/j.clinbiochem.2013.07.020 ◽

2013 ◽

Vol 46 (18) ◽

pp. 1783-1786 ◽

Cited By ~ 11

Author(s):

Karen Buysse ◽

Lean Beulen ◽

Ingrid Gomes ◽

Christian Gilissen ◽

Chantal Keesmaat ◽

...

Keyword(s):

Massively Parallel Sequencing ◽

Prenatal Testing ◽

Maternal Plasma ◽

Massively Parallel ◽

Noninvasive Prenatal Testing ◽

Cell Free Dna ◽

Parallel Sequencing ◽

Free Dna ◽

Circulating Cell Free Dna

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Novel OTOF gene mutations identified using a massively parallel DNA sequencing technique in DFNB9 deafness

Acta Oto-Laryngologica ◽

10.1080/00016489.2018.1476777 ◽

2018 ◽

Vol 138 (10) ◽

pp. 865-870 ◽

Cited By ~ 3

Author(s):

Yanfei Wang ◽

Yu Lu ◽

Jing Cheng ◽

Lei Zhang ◽

Dongyi Han ◽

...

Keyword(s):

Dna Sequencing ◽

Gene Mutations ◽

Massively Parallel ◽

Sequencing Technique ◽

Massively Parallel Dna Sequencing

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Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia

Blood ◽

10.1182/blood-2014-04-567933 ◽

2014 ◽

Vol 124 (3) ◽

pp. 453-462 ◽

Cited By ~ 202

Author(s):

Mohini Rajasagi ◽

Sachet A. Shukla ◽

Edward F. Fritsch ◽

Derin B. Keskin ◽

David DeLuca ◽

...

Keyword(s):

Chronic Lymphocytic Leukemia ◽

Dna Sequencing ◽

Lymphocytic Leukemia ◽

Class I ◽

Massively Parallel ◽

Central Tolerance ◽

Key Points ◽

Tumor Specificity ◽

Massively Parallel Dna Sequencing ◽

Systematic Identification

Key Points Tumor neoantigens are a promising class of immunogens based on exquisite tumor specificity and the lack of central tolerance against them. Massively parallel DNA sequencing with class I prediction enables systematic identification of tumor neoepitopes (including from CLL).

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