Evidence map›Paper›PMID 41831527›Full record

ArticleHuman pathology2026

The impact of next generation sequencing studies on the diagnosis of BAP1 inactivated melanocytic tumors.

Jonathan Braat, Nithya Sai Trichy, Lindsay Jeanne Holic, Shantel Olivares, Armita Bahrami, Thiagarajah Balamurugan, Raymond Barnhill, Willeke A M Blokx, Klaus J Busam, Lorenzo Cerroni and 23 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Human pathology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

33 authors.

Jonathan BraatDepartment of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
Nithya Sai TrichyDepartment of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
Lindsay Jeanne HolicDepartment of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
Shantel OlivaresDepartment of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
Armita BahramiDepartment of Pathology, Emory University School of Medicine, Atlanta, GA, USA.
Thiagarajah BalamuruganDepartment of Pathology, Royal Surrey NHS Foundation Trust, Guildford, UK.
Raymond BarnhillDepartment of Translational Research, Institut Curie, Paris Sciences and Lettres Research University, And UFR of Medicine, University of Paris Cité, Paris, France.
Willeke A M BlokxDepartment of Pathology, Division Laboratories, Pharmacy and Biomedical Genetics University Medical Center Utrecht, the Netherlands.
Klaus J BusamDepartment of Pathology, Dermatopathology Service, Memorial Sloan Kettering Cancer Center, New York City, NY, USA.
Lorenzo CerroniDepartment of Dermatology, Medical University of Graz, Graz, Austria.
Martin CookDepartment of Pathology, Royal Surrey NHS Foundation Trust, Guildford, UK.
Lyn DuncanDermatopathology Unit, Pathology Service, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
David ElderDepartment of Pathology and Laboratory Medicine, Division of Anatomic Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA.
Peter FergusonMelanoma Institute Australia, The University of Sydney, Sydney, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, and NSW Health Pathology, Sydney, NSW, Australia.
Gerardo FerraraAnatomic Pathology and Cytopathology Unit, Istituto Nazionale Tumori IRCCS Fondazione 'G. Pascale', Naples, Italy.
Jennifer KoDepartment of Anatomic Pathology, Cleveland Clinic, Cleveland, OH, USA.
Gilles LandmanDepartment of Pathology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.
Cecilia LezcanoDepartment of Pathology, Dermatopathology Service, Memorial Sloan Kettering Cancer Center, New York City, NY, USA.
Lori LoweDepartments of Dermatology and Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Daniela MassiDepartment of Health Sciences, Section of Anatomic Pathology, University of Florence, Florence, Italy.
Daniela Mihic-ProbstDepartment of Pathology and Molecular Pathology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland.
Douglas ParkerDepartments of Pathology and Dermatology, Emory University School of Medicine, Atlanta, GA, USA.
Michael SargenDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
Richard ScolyerMelanoma Institute Australia, The University of Sydney, Sydney, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, and NSW Health Pathology, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.
Christopher SheaDepartment of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA.
Alan SpatzDepartment of Pathology, McGill University, Montreal, Quebec, Canada.
Michael TetzlaffDermatopathology and Oral Pathology Unit, Departments of Pathology and Dermatology, University of California, San Francisco, San Francisco, CA, USA.
Carlos Antonio Torres-CabalaDepartments of Pathology and Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Victor TronDepartment of Dermatopathology, University of Toronto, Toronto, Ontario, Canada.
Iwei YehDivision of Dermatopathology, University of California San Francisco Medical Center, San Francisco, CA, USA.
Sook Jung YunDepartment of Dermatology, Chonnam National University Medical School, Gwangju, South Korea.
Artur ZembowiczDermatopathology Consultations LLC, Lahey Clinic, USA; Tufts Medical School, Boston, MA, USA.
Pedram GeramiDepartment of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. Electronic address: pedram.gerami@nm.org.

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026
$347.4M
Intramural NIH HHS Z99 CA999999NCI NIH HHS P30 CA008748
6 · The paper itself

Abstract

BAP1 inactivated melanocytic tumors (BIMTs) are recognized for their potential for significant morphologic atypia including nuclear atypia, expansile growth, and mitotic activity, making it difficult to form firm morphologic criteria for malignancy. Next generation sequencing (NGS) is becoming increasingly utilized in melanocytic pathology. We conducted a two-phase survey with 26 dermatopathologists from the International Melanoma Pathology Study Group to assess the impact of NGS on diagnostic accuracy and interobserver agreement in 31 BIMTs. After NGS results, interobserver agreement improved from fair on Survey 1 (κ = 0.348) to moderate on Survey 2 (κ = 0.441). Respondents were 1.7 times more likely to be correct on Survey 2 after NGS results (OR = 1.67, 95% CI [1.16-2.44], p = 0.005). When accounting for case variability and difficulty, respondents were 8.7 times more likely to provide a correct diagnosis for a given case (CMH OR = 8.69, 95% CI [4.89-15.44], p < 0.001). Among the 8 BAP1 inactivated melanomas in this study, 3 transitioned from a majority of votes for benign/intermediate grade BIMT to a majority of votes for melanoma after seeing NGS data. Genomic aberrations exclusive to malignant cases included pathogenic variants in TERT-p, CDKN2A, PTEN, and amplification of MYC. Our study suggests NGS has the potential to improve diagnostic accuracy and interobserver agreement for BAP1 inactivated melanocytic tumors. With the advent of increasingly effective therapies for melanoma, there is value in forming a definitive diagnosis of melanoma when appropriate. Additional studies with greater case numbers and follow-up are needed to further validate these findings.

Indexed as

Biomarkers, TumorHigh-Throughput Nucleotide SequencingMelanomaSkin NeoplasmsTumor Suppressor ProteinsUbiquitin ThiolesteraseDNA Mutational AnalysisFemaleGenetic Predisposition to DiseaseHumansMutationObserver VariationPredictive Value of TestsReproducibility of ResultsBAP1 protein, humanBiomarkers, TumorTumor Suppressor ProteinsUbiquitin ThiolesteraseBAP1BAP1 inactivated melanocytic tumorBAP1 inactivated melanocytomaBAP1 inactivated melanomaNext generation sequencing

Identifiers

PMID41831527
PMCPMC13396703

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.