Nature Search

Enhanced clinical assessment of hematologic malignancies through routine paired tumor and normal sequencing

Targeted sequencing panels such as MSK-IMPACT have been successfully used to profile solid tumours in clinical settings. Here, the authors develop and implement the MSK-IMPACT Heme sequencing panel and platform to profile haematologic malignancies using paired tumor and normal tissues.

Ryan N. Ptashkin
Mark D. Ewalt
Maria E. Arcila
ResearchOpen Access28 Oct 2023
Nature Communications

Volume: 14, P: 1-16
TDP-43 loss induces cryptic polyadenylation in ALS/FTD

The authors find that TDP-43 loss of function—the pathology defining the neurodegenerative conditions ALS and FTD—induces novel mRNA polyadenylation events, which have different effects, including an increase in RNA stability, leading to higher protein levels.

Sam Bryce-Smith
Anna-Leigh Brown
Pietro Fratta
ResearchOpen Access21 Oct 2025
Nature Neuroscience

Volume: 28, P: 2190-2200
Real-world deployment of a fine-tuned pathology foundation model for lung cancer biomarker detection

In a silent trial involving 197 patients with lung cancer over a span of 4 months, a fine-tuned pathology foundation model was able to identify the presence of EGFR mutations with high accuracy, potentially preventing further genetic testing in 43% of cases.

Gabriele Campanella
Neeraj Kumar
Chad Vanderbilt
ResearchOpen Access09 Jul 2025
Nature Medicine

Volume: 31, P: 3002-3010
Maximizing the clinical utility and performance of cytology samples for comprehensive genetic profiling

Tumour profiling with next-generation sequencing is challenging due to the low amounts of diagnostic material in cytology samples that are obtained through non-invasive procedures. Here, the authors report on the optimization of this process across 4,871 cancer cytology samples profiled by MSK-IMPACT, with emphasis on the successful use of supernatant cell-free DNA.

David Kim
Chad M. Vanderbilt
Maria E. Arcila
ResearchOpen Access02 Jan 2025
Nature Communications

Volume: 16, P: 1-11
DNA liquid biopsy-based prediction of cancer-associated venous thromboembolism

An analysis of three multi-cancer cohorts shows that the detection of ctDNA using liquid biopsies has the potential to improve the risk prediction of cancer-associated venous thromboembolism.

Justin Jee
A. Rose Brannon
Simon Mantha
ResearchOpen Access15 Aug 2024
Nature Medicine

Volume: 30, P: 2499-2507
Frequent somatic CDH1 loss-of-function mutations in plasmacytoid variant bladder cancer

David Solit and colleagues report that inactivating CDH1 mutations are found in 84% of plasmacytoid bladder cancer samples tested and are not found in other bladder cancer subtypes. CRISPR/Cas9-mediated knockout of CDH1 in cell lines leads to enhanced cellular migration.

Hikmat A Al-Ahmadie
Gopa Iyer
David B Solit
Research22 Feb 2016
Nature Genetics

Volume: 48, P: 356-358
Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell-free DNA via paired normal sequencing using MSK-ACCESS

Liquid biopsies allow the non-invasive detection of somatic mutations from tumours. Here, the authors develop and test MSK-ACCESS, an NGS-based clinical assay for identifying low frequency mutations in 129 genes and describe how it benefits patients in the clinic.

A. Rose Brannon
Gowtham Jayakumaran
Ryma Benayed
ResearchOpen Access18 Jun 2021
Nature Communications

Volume: 12, P: 1-12
Overall survival with circulating tumor DNA-guided therapy in advanced non-small-cell lung cancer

In a prospective international cohort of 1,127 patients with non-small-cell lung cancer and ctDNA-guided therapy, ctDNA detection was associated with shorter survival, independently of clinicopathologic features and metabolic tumor volume.

Justin Jee
Emily S. Lebow
Bob T. Li
Research10 Nov 2022
Nature Medicine

Volume: 28, P: 2353-2363
ERBB2 amplification status in 67 salivary duct carcinomas assessed by immunohistochemistry, fluorescence in situ hybridization, and targeted exome sequencing

Donna C. Ferguson
Amir Momeni Boroujeni
Snjezana Dogan
Research28 Dec 2021
Modern Pathology

Volume: 35, P: 895-902
Androgen receptor splice variant-7 in breast cancer: clinical and pathologic correlations

Donna C. Ferguson
Douglas A. Mata
Dara S. Ross
Research30 Sept 2021
Modern Pathology

Volume: 35, P: 396-402
Cancer therapy shapes the fitness landscape of clonal hematopoiesis

Environmental exposures shape patterns of selection for mutations in clonal hematopoiesis. Cancer therapies promote the growth of clones with mutations that are strongly enriched in treatment-related myeloid neoplasms.

Kelly L. Bolton
Ryan N. Ptashkin
Elli Papaemmanuil
Research26 Oct 2020
Nature Genetics

Volume: 52, P: 1219-1226
Multinational proficiency tests for EGFR exon 20 insertions reveal that the assay design matters

Michaela A. Ihle
Carina Heydt
Sabine Merkelbach-Bruse
ResearchOpen Access06 Jun 2024
Scientific Reports

Volume: 14, P: 1-11
Erratum: Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients

Ahmet Zehir
Ryma Benayed
Michael F Berger
Amendments and Corrections04 Aug 2017
Nature Medicine

Volume: 23, P: 1004
TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A

Risk variants for ALS and FTD in the synaptic gene UNC13A increase the expression of an UNC13A cryptic exon in neurons with TDP-43 depletion.

Anna-Leigh Brown
Oscar G. Wilkins
Pietro Fratta
ResearchOpen Access23 Feb 2022
Nature

Volume: 603, P: 131-137
Activation of the AXL kinase causes resistance to EGFR-targeted therapy in lung cancer

Trever Bivona and colleagues identify the upregulation of the AXL kinase in human non–small cell lung cancer with acquired resistance to erlotinib. Inhibition of AXL restores sensitivity to erlotinib in in vitro and in vivo tumor models. The authors suggest AXL as a potential therapeutic target that may prevent or overcome acquired resistance in patients with EGFR-mutant lung cancer.

Zhenfeng Zhang
Jae Cheol Lee
Trever G Bivona
Research01 Jul 2012
Nature Genetics

Volume: 44, P: 852-860
Activating mutations in CSF1R and additional receptor tyrosine kinases in histiocytic neoplasms

Inhibition of CSF-1R with recurrent activating alterations and other actionable targets identified by genomic sequencing elicits clinical activity in patients with histiocytosis.

Benjamin H. Durham
Estibaliz Lopez Rodrigo
Omar Abdel-Wahab
Research25 Nov 2019
Nature Medicine

Volume: 25, P: 1839-1842
Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients

MSK-IMPACT is a clinical sequencing platform able to detect genomic mutations, copy number alterations and structural variants in a panel of cancer-related genes. This assay is implemented prospectively to inform patient enrollment in genomically matched clinical trials at Memorial Sloan Kettering Cancer Center (MSKCC). Sequencing results of tumor and matched normal tissue from a cohort of >10,000 patients with detailed clinical annotation provide an overview of the genomic landscape of advanced solid cancers and bring new insights into molecularly guided cancer therapy.

Ahmet Zehir
Ryma Benayed
Michael F Berger
Research08 May 2017
Nature Medicine

Volume: 23, P: 703-713
Genomic characterization of tumor mutational burden-high breast carcinomas

Theodore Vougiouklakis
Chad Vanderbilt
Dara S. Ross
ResearchOpen Access08 Aug 2025
npj Precision Oncology

Volume: 9, P: 1-11
Optical and theoretical study of strand recognition by nucleic acid probes

Nucleic acid probes that bind to cancer-related genes have potential as diagnostic tools. Here parameters governing the binding of locked nucleic acid probes to three oncogenes, including effects of molecular crowding and polyelectrolytes, are characterized and used to inform the design of a bead-bait RNA genotyping assay.

Ivana Domljanovic
Maria Taskova
Kira Astakhova
ResearchOpen Access11 Aug 2020
Communications Chemistry

Volume: 3, P: 1-13
Identifying patterns in amyotrophic lateral sclerosis progression from sparse longitudinal data

A machine learning approach is presented to identify dominant patterns in disease progression in amyotrophic lateral sclerosis (ALS), Alzheimer’s disease and Parkinson’s disease. The nonlinearity of ALS progression has important clinical implications.

Divya Ramamoorthy
Kristen Severson
Ernest Fraenkel
ResearchOpen Access08 Sept 2022
Nature Computational Science

Volume: 2, P: 605-616
Acquired resistance to IDH inhibition through trans or cis dimer-interface mutations

A new mechanism of acquired clinical resistance in two patients with acute myeloid leukaemia driven by mutant IDH2 is described, in which a second-site mutation on the wild-type allele induces therapeutic resistance to IDH2 inhibitors.

Andrew M. Intlekofer
Alan H. Shih
Eytan M. Stein
Research27 Jun 2018
Nature

Volume: 559, P: 125-129
Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Maria Alejandra Serna-Sánchez
Oscar A. Pérez-Escobar
Tatiana Arias
ResearchOpen Access25 Mar 2021
Scientific Reports

Volume: 11, P: 1-11
DNMT3A mutations promote anthracycline resistance in acute myeloid leukemia via impaired nucleosome remodeling

AML cells carrying R882 mutations in DNMT3A fail to sense and repair DNA damage induced by standard-dose chemotherapy as a result of impaired chromatin remodeling

Olga A Guryanova
Kaitlyn Shank
Ross L Levine
Research14 Nov 2016
Nature Medicine

Volume: 22, P: 1488-1495
Author Correction: TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A

Anna-Leigh Brown
Oscar G. Wilkins
Pietro Fratta
Amendments and CorrectionsOpen Access18 Jun 2024
Nature

Volume: 631, P: E7
Genetic basis for iMCD-TAFRO

Akihide Yoshimi
Tanya M. Trippett
Wenbin Xiao
Research12 Feb 2020
Oncogene

Volume: 39, P: 3218-3225
JAK/MAP kinase pathway activation and TP53 mutations in acute leukemia with megakaryocytic and erythroid differentiation

Wenbin Xiao
Raajit Rampal
David C. Park
Research24 Apr 2018
Leukemia

Volume: 32, P: 1842-1845
Sequencing of 279 cancer genes in ampullary carcinoma reveals trends relating to histologic subtypes and frequent amplification and overexpression of ERBB2 (HER2)

Jaclyn F Hechtman
Weiguo Liu
David S Klimstra
Research15 May 2015
Modern Pathology

Volume: 28, P: 1123-1129
Reduced H3K27me3 expression in Merkel cell polyoma virus-positive tumors

Klaus J Busam
Melissa P Pulitzer
Thomas Wiesner
Research10 Mar 2017
Modern Pathology

Volume: 30, P: 877-883
MET-dependent solid tumours — molecular diagnosis and targeted therapy

Therapies targeting MET-overexpressing cancers have limited efficacy. However, owing to advances in detection methods, therapies targeting MET-dependent tumours harbouring MET amplifications, activating mutations or fusions are emerging. In this review, the authors describe emerging data on this new class of targeted therapies.

Robin Guo
Jia Luo
Alexander Drilon
Reviews08 Jun 2020
Nature Reviews Clinical Oncology

Volume: 17, P: 569-587
Erratum: Distinct profile of driver mutations and clinical features in immunomarker-defined subsets of pulmonary large-cell carcinoma

Natasha Rekhtman
Laura J Tafe
Marc Ladanyi
Amendments and Corrections02 Jan 2014
Modern Pathology

Volume: 27, P: 163
Prognostic impact of RAS-pathway mutations in patients with myelofibrosis

Fabio P. S. Santos
Bartlomiej Getta
Srdan Verstovsek
Research18 Oct 2019
Leukemia

Volume: 34, P: 799-810
JAK2/PD-L1/PD-L2 (9p24.1) amplifications in renal cell carcinomas with sarcomatoid transformation: implications for clinical management

Sounak Gupta
John C. Cheville
Victor E. Reuter
Research17 Apr 2019
Modern Pathology

Volume: 32, P: 1344-1358
Apoptosis characterization in mononuclear blood leukocytes of HIV patients during dengue acute disease

Amanda Torrentes-Carvalho
Juan Camilo Sánchez-Arcila
Elzinandes Leal de Azeredo
ResearchOpen Access14 Apr 2020
Scientific Reports

Volume: 10, P: 1-13
Author Correction: Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Maria Alejandra Serna-Sánchez
Oscar A. Pérez-Escobar
Tatiana Arias
Amendments and CorrectionsOpen Access06 Jul 2021
Scientific Reports

Volume: 11, P: 1-3
Engraftment kinetics after transplantation of double unit cord blood grafts combined with haplo-identical CD34+ cells without antithymocyte globulin

Ioannis Politikos
Sean M. Devlin
Juliet N. Barker
Research18 Jun 2020
Leukemia

Volume: 35, P: 850-862
Sclerosing epithelioid mesenchymal neoplasm of the pancreas – a proposed new entity

Olca Basturk
Britta Weigelt
David S. Klimstra
Research05 Aug 2019
Modern Pathology

Volume: 33, P: 456-467
Cell environment shapes TDP-43 function with implications in neuronal and muscle disease

The aetiology of the TDP-43 aggregation manifest itself in the muscle and neuronal cells. Here authors show cell-type characteristic functions of TDP43, reflected in aberrant splicing, likely contributing to disease development.

Urša Šušnjar
Neva Škrabar
Emanuele Buratti
ResearchOpen Access05 Apr 2022
Communications Biology

Volume: 5, P: 1-17
Baseline VDJ clonotype detection using a targeted sequencing NGS assay: allowing for subsequent MRD assessment

Malin Hultcrantz
Even Holth Rustad
Ola Landgren
CorrespondenceOpen Access22 Jul 2020
Blood Cancer Journal

Volume: 10, P: 1-3
Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis

Debra Van Egeren
Khushi Kohli
Zenta Walther
ResearchOpen Access09 Nov 2022
Scientific Reports

Volume: 12, P: 1-6
Distinct profile of driver mutations and clinical features in immunomarker-defined subsets of pulmonary large-cell carcinoma

Natasha Rekhtman
Laura J Tafe
Marc Ladanyi
Research30 Nov 2012
Modern Pathology

Volume: 26, P: 511-522

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