Chromatin accessibility profiling by ATAC-seq

FC Grandi, H Modi, L Kampman, MR Corces - Nature protocols, 2022 - nature.com
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a
simple and scalable way to detect the unique chromatin landscape associated with a cell …

Best practices for variant calling in clinical sequencing

DC Koboldt - Genome Medicine, 2020 - Springer
Next-generation sequencing technologies have enabled a dramatic expansion of clinical
genetic testing both for inherited conditions and diseases such as cancer. Accurate variant …

Immunopathological signatures in multisystem inflammatory syndrome in children and pediatric COVID-19

K Sacco, R Castagnoli, S Vakkilainen, C Liu… - Nature medicine, 2022 - nature.com
Abstract Pediatric Coronavirus Disease 2019 (pCOVID-19) is rarely severe; however, a
minority of children infected with severe acute respiratory syndrome coronavirus 2 (SARS …

The sequences of 150,119 genomes in the UK Biobank

BV Halldorsson, HP Eggertsson, KHS Moore… - Nature, 2022 - nature.com
Detailed knowledge of how diversity in the sequence of the human genome affects
phenotypic diversity depends on a comprehensive and reliable characterization of both …

Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA

R Vaisvila, VKC Ponnaluri, Z Sun… - Genome …, 2021 - genome.cshlp.org
Bisulfite sequencing detects 5mC and 5hmC at single-base resolution. However, bisulfite
treatment damages DNA, which results in fragmentation, DNA loss, and biased sequencing …

Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer

C Herberts, M Annala, J Sipola, SWS Ng, XE Chen… - Nature, 2022 - nature.com
Circulating tumour DNA (ctDNA) in blood plasma is an emerging tool for clinical cancer
genotyping and longitudinal disease monitoring. However, owing to past emphasis on …

Glioblastomas acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion

E Gangoso, B Southgate, L Bradley, S Rus… - Cell, 2021 - cell.com
Glioblastoma multiforme (GBM) is an aggressive brain tumor for which current
immunotherapy approaches have been unsuccessful. Here, we explore the mechanisms …

Lung cancer organoids analyzed on microwell arrays predict drug responses of patients within a week

Y Hu, X Sui, F Song, Y Li, K Li, Z Chen, F Yang… - Nature …, 2021 - nature.com
While the potential of patient-derived organoids (PDOs) to predict patients' responses to anti-
cancer treatments has been well recognized, the lengthy time and the low efficiency in …

The GenomeAsia 100K Project enables genetic discoveries across Asia

Nature, 2019 - nature.com
The underrepresentation of non-Europeans in human genetic studies so far has limited the
diversity of individuals in genomic datasets and led to reduced medical relevance for a large …

Curated variation benchmarks for challenging medically relevant autosomal genes

J Wagner, ND Olson, L Harris, J McDaniel… - Nature …, 2022 - nature.com
The repetitive nature and complexity of some medically relevant genes poses a challenge
for their accurate analysis in a clinical setting. The Genome in a Bottle Consortium has …