Publications

Highly Sensitive Blocker Displacement Amplification for Detection of Low-Level JAK2 Variant

The Journal of Applied Laboratory Medicine

February 10, 2023

Wang, Z., Weller, C., Pinto, A., Zhang, D. Y., Mularo, F., Tu, Z. T., Cheng, Y. W.

Designing highly multiplex PCR primer sets with Simulated Annealing Design using Dimer Likelihood Estimation (SADDLE)

Nature Communications

April 11, 2022

Xie, N.G., Wang, M.X., Song, P., Mao, S., Wang, Y., Yang, Y., Luo, J., Ren, S. & Zhang, D.Y.

Ensemble of nucleic acid absolute quantitation modules for copy number variation detection and RNA profiling

Nature Communications

April 4, 2022

Wu, L. R., Dai, P., Wang, M. X., Chen, S. X., Cohen, E. N., Jayachandran, G., Zhang, J. X., Serrano, A. V., Xie, N.G., Ueno, N. T., Reuben, J. M., Barcenas, C. H. & Zhang, D. Y.

Single-Tube qPCR Detection and Quantitation of Hotspot Mutations Down to 0.01% Variant Allele Fraction

Analytical Chemistry

December 21, 2021

Zhang, K., Rodriguez, L., Cheng, L. Y., Wang, M., & Zhang, D. Y.

Calibration-free NGS quantitation of mutations below 0.01% VAF

Nature Communications

October 21, 2021

Dai, P., Wu, L.R., Chen, S.X, Wang, M.X., Chen, L.Y., Zhang, J.X., Hao, P., Yao, W., Zarka, J., Issa, G.C., Kwong, L. & Zhang, D.Y.

Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection

Genome Biology

September 06, 2021

Thirunavukarasu, D., Cheng, L.Y., Song, P., Chen, S.X., Borad, M.J., Kwong, L., James, P., Turner, D.J. & Zhang, D.Y.

Predicting stability of DNA bulge at mononucleotide microsatellite

Nucleic Acids Research

July 26, 2021

Bae, J.H., & Zhang, D.Y.

A deep learning model for predicting next-generation sequencing depth from DNA sequence

Nature Communications

July 19, 2021

Zhang, J.X., Yordanov, B., Gaunt, A., Wang, M.X., Dai, P., Chen., Y-J., Zhang, K., Fang, J.Z., Dalchau, N., Li, J., Phillips, A., & Zhang, D.Y.

Confirming putative variants at ≤ 5% allele frequency using allele enrichment and Sanger sequencing

Nature Scientific Reports

June 2, 2021

Yan, Y.H., Chen, S.X., Cheng, L.Y., Rodriguez, A.Y., Tang, R., Cabrera, K., & Zhang, D.Y.

Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing

NATURE BIOMEDICAL ENGINEERING

May 3, 2021

Song, P., Chen, S.X., Yan, Y.H., Pinto, A., Cheng, L.Y., Dai, P., Patel, A.A., & Zhang, D.Y.

High sensitivity sanger sequencing detection of BRAF mutations in metastatic melanoma FFPE tissue specimens

Nature Scientific Reports

April 27, 2021

Cheng, L.Y., Haydu, L.E., Song, P., Nie, J., Tetzlaff, M.T., Kwong, L.N., Gershenwald, J.E., Davies, M.A. & Zhang, D.Y.,

Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions

GENETICS IN MEDICINE

July 13, 2020

Gambin, T., …Xie, N.G., Wu L.R., Yan, Y.H., … Zhang, D.Y.,… Stankiewicz, P.

Highly sensitive blocker displacement amplification and droplet digital PCR reveal very low-level parental FOXF1 somatic mosaicism in families with ACDMPV

THE JOURNAL OF MOLECULAR DIAGNOSTICS

Feb 7, 2020

Karolak, J.A., Liu, Q., Xie, N.G., Wu L.R., …, Zhang, D.Y., Stankiewicz P.

A recurrent 8 bp frameshifting indel in FOXF1 defines a novel mutation hotspot associated with alveolar capillary dysplasia with misalignment of pulmonary veins.

AMERICAN JOURNAL OF MEDICAL GENETICS

Aug 22, 2019

Karolak, J.A., Bacolla, A., Liu, Q., Lantz, P.E., …, Zhang, D.Y., & Stankiewicz, P.

A preexisting rare PIK3CAE545K subpopulation confers clinical resistance to MEK plus CDK4/6 inhibition in NRAS melanoma and is dependent on S6K1 signaling.

CANCER DISCOVERY

Mar 1, 2018

Romano, G., Chen, P.L., Song, P., McQuade, J.L., …, Wargo, J.A., & Kwong, L.N.

Multiplexed enrichment of rare DNA variants via sequence-selective and temperature-robust amplification.

NATURE BIOMEDICAL ENGINEERING

Sept 4, 2017

Wu, L.R., Chen, S.X., Wu, Y., Patel, A.A., & Zhang, D.Y.

Optimizing the specificity of nucleic acid hybridization.

NATURE CHEMISTRY

Jan 22, 2012

Zhang, D. Y., Chen, S. X., & Yin, P.