Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing.

Nature Protocols
Peter EllisPeter J Campbell


Somatic mutations accumulate in healthy tissues as we age, giving rise to cancer and potentially contributing to ageing. To study somatic mutations in non-neoplastic tissues, we developed a series of protocols to sequence the genomes of small populations of cells isolated from histological sections. Here, we describe a complete workflow that combines laser-capture microdissection (LCM) with low-input genome sequencing, while circumventing the use of whole-genome amplification (WGA). The protocol is subdivided broadly into four steps: tissue processing, LCM, low-input library generation and mutation calling and filtering. The tissue processing and LCM steps are provided as general guidelines that might require tailoring based on the specific requirements of the study at hand. Our protocol for low-input library generation uses enzymatic rather than acoustic fragmentation to generate WGA-free whole-genome libraries. Finally, the mutation calling and filtering strategy has been adapted from previously published protocols to account for artifacts introduced via library creation. To date, we have used this workflow to perform targeted and whole-genome sequencing of small populations of cells (typically 100-1,000 cells) in thousands o...Continue Reading


Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Jul 6, 2010·Nucleic Acids Research·Kai WangHakon Hakonarson
Sep 15, 2010·Proceedings of the National Academy of Sciences of the United States of America·Peter Van LooVessela N Kristensen
Jan 5, 2014·Nature Protocols·Simone PicelliRickard Sandberg
Oct 10, 2014·Nature Protocols·Scott R KennedyLawrence A Loeb
Jan 26, 2016·Nature Reviews. Genetics·Charles GawadStephen R Quake
Feb 26, 2016·Nature Cell Biology·Aliya FatehullahNick Barker
Jul 13, 2016·American Journal of Clinical Pathology·William MathiesonGeraldine A Thomas
Aug 17, 2016·Proceedings of the National Academy of Sciences of the United States of America·Margaret L HoangNickolas Papadopoulos
Oct 5, 2016·Nature·Francis BlokzijlRuben van Boxtel
Dec 9, 2016·Current Protocols in Bioinformatics·David JonesPeter J Campbell
Sep 7, 2018·Nature·Henry Lee-SixPeter J Campbell
Oct 20, 2018·Science·Iñigo MartincorenaPhilip H Jones
Oct 28, 2019·Nature·Simon F BrunnerPeter J Campbell
Oct 28, 2019·Nature·Henry Lee-SixMichael R Stratton
Jan 31, 2020·Nature·Kenichi YoshidaPeter J Campbell
May 1, 2020·Nature·Luiza MooreMichael R Stratton
Jul 23, 2020·Cell·Sigurgeir OlafssonCarl A Anderson

❮ Previous
Next ❯


Apr 30, 2021·Nature·Federico AbascalIñigo Martincorena
May 14, 2021·Nature·Michael Spencer ChapmanAna Cvejic
Jul 7, 2021·Trends in Genetics : TIG·Sigurgeir Olafsson, Carl A Anderson
Aug 27, 2021·Nature·Luiza MooreRaheleh Rahbari
Aug 27, 2021·Nature·Tim H H CoorensMichael R Stratton
Oct 2, 2021·Nature Genetics·Philip S RobinsonMichael R Stratton
Oct 15, 2021·Nature·Stanley W K NgPeter J Campbell
Oct 12, 2021·Nucleic Acids Research·Shixiang SunJan Vijg

❮ Previous
Next ❯

Methods Mentioned

single-cell sequencing
exome sequencing

Software Mentioned

GATK package

Related Concepts

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.


Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.


Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.