Targeted sequencing of 252 genes based on their relevance in lymphoid malignancies
type: Dataset
description: Dataset description Data consists of CRAM file from capture-based gene panel sequencing (Twist Bioscience) of 252 genes selected based on their relevance in lymphoid malignancies. The panel also included genome-wide backbone probes for copy-number analysis. The preprared libraries were then subsequenlty equenced in paired-end mode (2x150bp) on the Illumina NovaSeq 6000 (Illumina Inc.). BALSAMIC was used to analyze the FASTQ files and aligning them to reference genome. Trimmed reads were mapped to the reference genome hg19 using BWA MEM v0.7.15 4. The resulting SAM files were converted to BAM files and sorted using samtools v1.6. Duplicated reads were marked using Picard tools MarkDuplicate v2.17.0. And finally converted to CRAM files using samtools v1.6. Note: CRAM is a sequencing read file format that is highly space efficient by using reference-based compression of sequence data and offers both lossless and lossy modes of compression: https://www.ebi.ac.uk/ena/cram/ Data Access Statement The data is under restricted access and can be accessed upon request through the email-adress below. The targeted sequence datasets are only to be used for research aimed at advancing the understanding of genetic factors in the chronic lymphocytic leukemia. Applications aimed at method development including bioinformatics would not be considered as acceptable for use of this dataset.
conditions of access: https://publications.europa.eu/resource/authority/access-right/NON_PUBLIC
conditions of access: info:eu-repo/semantics/restrictedAccess
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Silvia Bonfiglio
  type: Person
  family name: Bonfiglio
  given name: Silvia
creator: Lesley-Ann Sutton
  type: Person
  family name: Sutton
  given name: Lesley-Ann
creator: Viktor Ljungström
  type: Person
  affiliation: Science for Life Laboratory
  family name: Ljungström
  given name: Viktor
creator: Antonella Capasso
  type: Person
  family name: Capasso
  given name: Antonella
creator: Tatjana Pandzic
  type: Person
  family name: Pandzic
  given name: Tatjana
creator: Simone Weström
  type: Person
  family name: Weström
  given name: Simone
creator: Hassan Foroughi Asl
creator: Aron Skaftason
  type: Person
  family name: Skaftason
  given name: Aron
creator: Anna Gellerbring
  type: Person
  family name: Gellerbring
  given name: Anna
creator: Anna Lyander
  type: Person
  family name: Lyander
  given name: Anna
creator: Francesca Gandini
  type: Person
  family name: Gandini
  given name: Francesca
creator: Gianluca Gaidano
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  family name: Gaidano
  given name: Gianluca
creator: Livio Trentin
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  family name: Trentin
  given name: Livio
creator: Lisa Bonello
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  family name: Bonello
  given name: Lisa
creator: Gianluigi Reda
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  family name: Reda
  given name: Gianluigi
creator: Csaba Bodor
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creator: Niki Stravoyianni
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  family name: Stravoyianni
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creator: Costantine S. Tam
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  given name: Costantine S.
creator: Roberto Marasca
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creator: Francesco Forconi
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  given name: Francesco
creator: Panayiotis Panayiotidis
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  family name: Panayiotidis
  given name: Panayiotis
creator: Ingo Ringshausen
  type: Person
  family name: Ringshausen
  given name: Ingo
creator: Ozren Jakšić
creator: Alessandra Tedeschi
  type: Person
  family name: Tedeschi
  given name: Alessandra
creator: Anna Maria Frustaci
  type: Person
  family name: Frustaci
  given name: Anna Maria
creator: Sunil Iyengar
  type: Person
  family name: Iyengar
  given name: Sunil
creator: Marta Coscia
  type: Person
  family name: Coscia
  given name: Marta
creator: Stephen P. Mulligan
  type: Person
  family name: Mulligan
  given name: Stephen P.
creator: Loïc Ysebaert
  type: Person
  family name: Ysebaert
  given name: Loïc
creator: Vladimir Strugov
  type: Person
  family name: Strugov
  given name: Vladimir
creator: Carolina Pavlovsky
  type: Person
  family name: Pavlovsky
  given name: Carolina
creator: Zadie Davis
  type: Person
  family name: Davis
  given name: Zadie
creator: Anders Österborg
  type: Person
  family name: Österborg
  given name: Anders
creator: Diego Cortese
  type: Person
  family name: Cortese
  given name: Diego
creator: Pamela Ranghetti
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  family name: Ranghetti
  given name: Pamela
creator: Panagiotis Baliakas
  type: Person
  family name: Baliakas
  given name: Panagiotis
creator: Kostas Stamatopoulos
  type: Person
  family name: Stamatopoulos
  given name: Kostas
creator: Lydia Scarfò
  type: Person
  family name: Scarfò
  given name: Lydia
creator: Richard Rosenquist Brandell
  type: Person
  affiliation: Science for Life Laboratory
  family name: Rosenquist Brandell
  given name: Richard
creator: Paolo Ghia
  type: Person
  family name: Ghia
  given name: Paolo
date modified: 2023-05-31
date published: 2022-05-12
keywords: Medical and Health Sciences
  type: DefinedTerm
  term code: 3
keywords: Hematology
  type: DefinedTerm
  term code: 30202
keywords: Cancer and Oncology
  type: DefinedTerm
  term code: 30203
keywords: Cancer genetics
keywords: Cancer diagnosis
keywords: Haematology
publisher: Karolinska Institutet
version: 0

PropertyValue
property ID: DOI
value: 10.17044/SCILIFELAB.19721998

Science for Life Laboratory
type: Organization

Hassan Foroughi Asl
type: Person
affiliation: Science for Life Laboratory
family name: Foroughi Asl
given name: Hassan

Ozren Jakšić
type: Person
family name: Jakšić
given name: Ozren

Karolinska Institutet
type: Organization