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Whole Genome and Transcriptome

Analysis of Anaplastic Meningioma

Patrick TarpeyCancer Genome Project

Wellcome Trust Sanger Institute

• Anaplastic meningioma compared to other cancers

• Whole genomes inform diagnosis

• Landscape of driver variants

• Identification of clinically relevant sub-types

Outline

Meningioma

• Most common primary central nervous system tumours in adults

• Originate from the meningeal membrane covering the brain and spinal cord

• Classified as:

Grade 1: benign (70-80%)

Grade 2: atypical (5-20%)

Grade 3: malignant (1-3%)

Anaplastic Meningioma

• Presentation: progression of lower grade tumour or de novo

• Prognosis: poor, many cases inevitable recurrence

• Current insight:

Grade 1 and 2: well characterised

Grade 3: poorly understood, limited therapeutic options

Study Design

• Discovery cohort (whole genomes)Paired FF DNA

• Extension cohort (known cancer genes)Paired and unpaired, FF and FFPE

Discovery Cohort

Discovery Cohort

Extension Cohort

Point mutations

• Coding exons from 366 genes (CGC)

• 333 probes targeting actionable loci (KRAS, BRAF, EGFR, ALK, KIT, TP53)

• TERT promoter

Fusions

• 2462 probes targeting 29 fusions involving 11 genes

Copy number

• 1912 probes targeting 961 reference SNPs (1 SNP per 3Mb)

• 1114 probes targeting SNPs in frequently amplified genes

Solid tumour panel (52,461 probes, 2.05 Mb)

genefusions

SNPgwas

SNPcytoscape

SNPintrons

Copynumber

exons,366genes7941regions

• Anaplastic meningioma compared to other cancers

• Whole genomes inform diagnosis

• Landscape of driver variants

• Identification of clinically relevant sub-types

Outline

Whole Genomes: point mutations

subs

indels

subs (snp id)

Whole Genomes: mutation burden

Sanger Analysis

PipelineCore Sequencing Facility

MappingBWA-mem

Fastq Raw Data

Downstream AnalysisIdentification of Driver mutations & cancer genes, subclonal mutations etc

Bam Coverage stats

CopyNumber

CNVkit

Genefusions

PointMutations

Indels

Brass

Cavemanvcf

Pindelvcf

Annotation:Vagrent

50bptrim

Report

Whole Genomes: mutation burden

Universal Patterns Of Selection In Cancer And Somatic Tissues

Inigo Martincorena

AM (n=19)

NF2

• Anaplastic meningioma compared to other cancers

• Whole genomes inform diagnosis

• Landscape of driver variants

• Identification of clinically relevant sub-types

Outline

Whole Genomes: atypical cases

subs

indels

subs (snp id)

``̀`

NF2 mut

``̀`

NF2 wt

MS

I

``̀`

NAB2-

STAT6

NF2 wt

``̀`

NAB2-

STAT6

NF2 wt

``̀`

NF2 wt

EML4-

ALK

``̀`

NF2 wt

EML4-

ALK

Discovery Cohort

• Anaplastic meningioma compared to other cancers

• Whole genomes inform diagnosis

• Landscape of driver variants

• Identification of clinically relevant sub-types

Outline

Supplementary Figure S4

a

b

Supplementary Figure S4 | Rearrangement burden of anaplastic meningioma. (a) Rearrangement subtypes in

18 primary anaplastic meningioma genomes classified into four broad categories of structural variant. The horizontal

axis indicates sample number and the vertical axis shows the total number of rearrangements. (b) Comparison of

overall rearrangement burden in anaplastic meningioma with 11 other tumor types colour coded according to source

of data and analysis. Horizontal axis indicates cancer type and number of samples per cohort. Vertical axis shows

rearrangent number per sample. Box plot hinges demarcate the 25th to 75th centile with median indicated by the

middle horizonal line and whiskers extending to 1.5 times the interquartile range. Underlying violin plots show the full

range and distribution of rearrangement burden across each tumor cohort. WTSI, Wellcome Trust Sanger Institute.

Supplementary Figure S4

a

b

Supplementary Figure S4 | Rearrangement burden of anaplastic meningioma. (a) Rearrangement subtypes in

18 primary anaplastic meningioma genomes classified into four broad categories of structural variant. The horizontal

axis indicates sample number and the vertical axis shows the total number of rearrangements. (b) Comparison of

overall rearrangement burden in anaplastic meningioma with 11 other tumor types colour coded according to source

of data and analysis. Horizontal axis indicates cancer type and number of samples per cohort. Vertical axis shows

rearrangent number per sample. Box plot hinges demarcate the 25th to 75th centile with median indicated by the

middle horizonal line and whiskers extending to 1.5 times the interquartile range. Underlying violin plots show the full

range and distribution of rearrangement burden across each tumor cohort. WTSI, Wellcome Trust Sanger Institute.

Rearrangements

• No recurrent novel fusions

• Disruptive rearrangements in PBRM1 and RB1

Copy Number

Aggregate CN profiles from 18 genomes

• Multiple recurrent CN changes

deletions: 1p, 6q, 14 and 22

• Homozygous deletion: NF2 and CDKN2A

Drivers

• Anaplastic meningioma compared to other cancers

• Whole genomes inform diagnosis

• Landscape of driver variants

• Identification of clinically relevant sub-types

Outline

31 tumours, 28 patients

31 tumours, 28 patients 25 patients

100%

62%

C1 C2

50%

0%

C1 C2

NF2 ARID1A, PBRM1

31 tumours, 28 patients 25 patients

Acknowledgements