Search Publications » Featured Publications

Featured Publication

DNA sequencing versus standard prenatal aneuploidy screening

Investigators compared standard aneuploidy screening to the verifi prenatal test, a non-invasive prenatal testing method that sequences maternal cell-free DNA. The verifi test demonstrated a significantly lower rate of false positives and higher positive predictive values for the detection of trisomies 18 and 21 compared to standard screening. The test performed consistently, regardless of each individual's risk level for fetal aneuploidy.
Read more at PubMed »
Featured Publication

Identification of low-frequency and rare sequence variants associated with elevated or reduced risk of type 2 diabetes

To investigate low-frequency variants that impact the risk for type 2 diabetes, researchers sequenced the genomes of 2,630 individuals. They statistically imputed identified SNPs and indels into additional cases and controls and examined the association between variants and the disease. Analysis revealed four novel variants affecting the risk level for type 2 diabetes.
Read more at PubMed »
Featured Publication

Whole-genome haplotyping using long reads and statistical methods

Researchers developed a statistically aided, long-read haplotyping (SLRH) method, which uses an algorithm to perform whole-genome haplotyping. They used SLRH to phase SNPs, determine allele-specific methylation patterns, and identify novel differentially methylated regions in a human genome.
Read more at PubMed »
Featured Publication

Finding the needle in the haystack: Differentiating "identical" twins in paternity testing and forensics by ultra-deep next generation sequencing

Microsatellite-based DNA tests currently used for paternity testing and forensic identification cannot distinguish between monozygotic twins. Deep sequencing of a pair of twins revealed five rare mutations that were used to differentiate between the two individuals. This finding may influence the development of alternate methods for DNA-based identification.
Read more at PubMed »
DNA sequencing versus standard prenatal aneuploidy screening
Identification of low-frequency variants associated with risk of type 2 diabetes
Whole-genome haplotyping using long reads and statistical methods
Differentiating "identical" twins in paternity testing and forensics by ultra-deep sequencing

Comprehensive molecular characterization of urothelial bladder carcinoma

Researchers from The Cancer Genome Atlas Research Network analyzed 131 cancer specimens to provide a comprehensive landscape of molecular alterations in urothelial bladder carcinoma. Whole-genome and RNA sequencing identified recurrent mutations and expression patterns, indicating potential targets for therapeutic development.

Read more at PubMed »

Cancer Genome Atlas Research Network Comprehensive molecular characterization of urothelial bladder carcinoma  Nature

Identification of low-frequency and rare sequence variants associated with elevated or reduced risk of type 2 diabetes

To investigate low-frequency variants that impact the risk for type 2 diabetes, researchers sequenced the genomes of 2,630 individuals. They statistically imputed identified SNPs and indels into additional cases and controls and examined the association between variants and the disease. Analysis revealed four novel variants affecting the risk level for type 2 diabetes.

Read more at PubMed »

Steinthorsdottir V, Thorleifsson G, Sulem P, Helgason H, Grarup N, et al. Identification of low-frequency and rare sequence variants associated with elevated or reduced risk of type 2 diabetes  Nature Genetics

Finding the needle in the haystack: Differentiating "identical" twins in paternity testing and forensics by ultra-deep next generation sequencing

Microsatellite-based DNA tests currently used for paternity testing and forensic identification cannot distinguish between monozygotic twins. Deep sequencing of a pair of twins revealed five rare mutations that were used to differentiate between the two individuals. This finding may influence the development of alternate methods for DNA-based identification.

Read more at PubMed »

Weber-Lehmann J, Schilling E, Gradl G, Richter DC, Wiehler J, et al. Finding the needle in the haystack: Differentiating "identical" twins in paternity testing and forensics by ultra-deep next generation sequencing  Forensic Science International: Genetics

DNA sequencing versus standard prenatal aneuploidy screening

Investigators compared standard aneuploidy screening to the verifi prenatal test, a non-invasive prenatal testing method that sequences maternal cell-free DNA. The verifi test demonstrated a significantly lower rate of false positives and higher positive predictive values for the detection of trisomies 18 and 21 compared to standard screening. The test performed consistently, regardless of each individual's risk level for fetal aneuploidy.

Read more at PubMed »

Bianchi DW, Parker RL, Wentworth J, Madankumar R, Saffer C, et al. DNA sequencing versus standard prenatal aneuploidy screening  New England Journal of Medicine

Whole-genome haplotyping using long reads and statistical methods

Researchers developed a statistically aided, long-read haplotyping (SLRH) method, which uses an algorithm to perform whole-genome haplotyping. They used SLRH to phase SNPs, determine allele-specific methylation patterns, and identify novel differentially methylated regions in a human genome.

Read more at PubMed »

Kuleshov V, Xie D, Chen R, Pushkarev D, Ma Z, Klauwkamp T, et al. Whole-genome haplotyping using long reads and statistical methods  Nature Biotechnology

Clinical whole-genome sequencing in severe early-onset epilepsy reveals new genes and improves molecular diagnosis

Many metabolic and electro-physiological processes are implicated in severe early-onset epilepsy, complicating molecular genetic diagnosis. Clinical whole-genome sequencing of patients with severe early-onset epilepsy uncovered novel mutations and genetic mechanisms that may contribute to the disease.

Read more at PubMed »

Martin HC, Kim GE, Pagnamenta AT, Murakami Y, Carvill GL, et al. Clinical whole-genome sequencing in severe early-onset epilepsy reveals new genes and improves molecular diagnosis  Human Molecular Genetics

RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia

Some acute lymphoblastic leukemia (ALL) cases are characterized by the ETV6-RUNX1 fusion gene, but the gene alone is not sufficient to cause the disease. To investigate the somatic mutations that drive leukemia in conjunction with ETV6-RUNX1, researchers performed exome and whole-genome sequencing of ALL patients. Results identified RAG-mediated rearrangements as the dominant mutational process leading to ETV6-RUNX1 ALL.

Read more at PubMed »

Papaemmanuil E, Rapado I, Li Y, Potter NE, Wedge DC, et al. RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia  Nature Genetics

Diet rapidly and reproducibly alters the human gut microbiome

Researchers sequenced the gut microbiomes of 11 individuals who maintained either plant- or animal-based diets. Analysis indicated that the animal-based diet had a greater impact on microbial composition, increasing the abundance of bile-tolerant organisms and decreasing the levels of Firmicutes species. Results demonstrated that the human gut microbiota can respond rapidly to altered diet and may contribute to gastrointestinal disease.

Read more at PubMed »

David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, et al. Diet rapidly and reproducibly alters the human gut microbiome  Nature