PT  - JOURNAL ARTICLE
AU  - David S. Tsao
AU  - Sukrit Silas
AU  - Brian P. Landry
AU  - Nelda Itzep
AU  - Amy B. Nguyen
AU  - Celeste K. Kanne
AU  - Vivien A. Sheehan
AU  - Rani Sharma
AU  - Rahul Shukla
AU  - Prem N. Arora
AU  - Oguzhan Atay
TI  - A novel high-throughput molecular counting method with single base-pair resolution enables accurate single-gene NIPT
AID  - 10.1101/597732
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 597732
4099  - http://biorxiv.org/content/early/2019/04/03/597732.short
4100  - http://biorxiv.org/content/early/2019/04/03/597732.full
AB  - Next-generation DNA sequencing is currently limited by an inability to count the number of input DNA molecules. Molecular counting is particularly needed when accurate quantification is required for diagnostic purposes, such as in single-gene non-invasive prenatal testing (sgNIPT) and liquid biopsy. We developed Quantitative Counting Template (QCT) molecular counting for reconstructing the number of input DNA molecules using sequencing data. We then used QCT molecular counting to develop sgNIPT of sickle cell disease, cystic fibrosis, spinal muscular atrophy, alpha-thalassemia, and beta-thalassemia. Incorporating molecular count information into a statistical model of disease likelihood led to analytical sensitivity and specificity of >98% and >99%, respectively. Validation of sgNIPT was further performed with maternal blood samples collected during pregnancy, and sgNIPT was 100% concordant with newborn follow-up.