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BaseSpace Knowledge Network
Variant interpretation is simplified with biomarker content curated from public databases.
Introduction
Estimates of human genome variants implicated in disease range inthe millions, yet many variants found in next-generation sequencing(NGS) studies are of unknown function or impact. The ability toprovide a relevant and contextualized report from NGS data
increasingly relies on knowledge bases, or repositories of curated
content for variants. To address this challenge, Illumina offers
BaseSpace Knowledge Network, a private knowledge base where
researchers can curate information about variants and attachdetailed supporting evidence. The BaseSpace Knowledge Networkcompiles information from public databases to help labs get started
with baseline content. Designed to allow a high degree ofcollaboration between team members within a workgroup andencourage curation best practices, the BaseSpace Knowledge
Network can reduce the time for interpretation while increasing theaccuracy and consistency of results.
The BaseSpace Knowledge Network is part of the Illumina
BaseSpace Informatics Suite, which also includes BaseSpace
Variant Intepreter (Beta). Together these products streamline
prioritization, interpretation, and reporting of genomic variants inhuman samples (Figure 1). Exclusively integrated with BaseSpace
Variant Interpreter (Beta), the BaseSpace Knowledge Network rapidly
accelerates manual interpretation of variants by providing highquality, curated content in the form of associations between genomicvariations and phenotypes (Figure 2). BaseSpace Variant Interpreter(Beta) provides a complete variant analysis workflow that includes
annotation, filtering, interpretation, and reporting.

the first knowledge bases of the BaseSpace Knowledge Network,
which connects individual knowledge bases to a standardized, highperformance network, and enables rapid sharing of variantinterpretations. More knowledge bases will be added in the future. In
this technical note, the curation process for each type of biomarker isdescribed, with a summary of the total number of associations.

Applying Years of Expertise inVariant Interpretation
The Illumina Biomedical Informatics team, originally part of NextBio™
Clinical, has invested years of time and expertise into building acontent set with hosted infrastructure, and a robust process to amass
high-quality variant interpretations. The content consists ofassociations between genomic variants and phenotypes for somaticand germline variants. The adopted curation process at Illumina
captures relevant information in standardized and structured ways toenable reporting. The purpose of curation is to harmonize thelanguage, contextualize the value, and trace the evidence for eachmarker. In this initial release, the content curated by Illumina includes
associations with single-nucleotide variants (SNVs), multinucleotide
variants (MNVs), and small insertions/deletions (indels).

Ontologies for Phenotypes and Drugs
The phenotype and drug information included for each genetic
variant is based on a modified Systematized Nomenclature of2Medicine (SNOMED) ontology for disease, and Medical Subject
3Headings (MESH) for drugs.

Variant associations are sourced from the Illumina Knowledge Base,1and the ClinVar database. Illumina Knowledge Base contains
expert-curated content from the Illumina Biomedical Informatics
team, and ClinVar, a National Institute of Health (NIH) funded initiativeFigure 1: BaseSpace Informatics Suite—A comprehensive series of genomics solutions offering continuous support for researchers from sample collection to final reports.
Beta versions of BaseSpace Variant Interpreter (Beta) and BaseSpace Knowledge Network are now available.

to facilitate sharing of variant interpretations. These sources represent

For Research Use Only. Not for use in diagnostic procedures.

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Figure 2: BaseSpace Variant Interpreter (Beta) and BaseSpace Knowledge Network—Both software platforms are integrated to decrease time and effort required forassociating variants with data curated from previous studies.

Somatic Biomarker Curation Process

Interpretation

Somatic mutations are acquired genetic alterations in somatic tissue
that are not transmitted to offspring. These mutations can be linked toa specific condition or be the underlying cause for cancer (drivermutation). Evidence-based summaries for somatic alterations are
harvested from publications, guidelines, drug labels, clinical trials, andapproved companion tests. The curation process uses anestablished workflow that identifies both emerging and establishedvariants to add to the Illumina Knowledge Base. Internal tracking andformal review steps ensure that each variant interpretation isconsistent with established protocols. Curated information isstructured around 4 major components: genetic variants, tumor
types/drugs tested, evidence summary, and evidence types (Figure3).

Somatic variant associations in cancer are categorized according totheir utility (Table 1):l

Predictive associations describe variants potentially responsive to
specific drug treatments, usually compared to standard therapies.

lPrognostic associations suggest that variants affect the rate of
disease progression over time.

lClassification associations suggest that variants are related todisease subtyping; these associations are often found in thepathological correlations sections of clinical research papers.

lClinical trial associations are established when variants have been
mentioned in inclusion criteria or as part of a trial design. Variants
can be specified (gene/codon) or implied (activity or drugsensitivity). All implied variants require additional evidence, such asa functional study establishing the effect of the alteration.

Figure 3: Variant Entry—Example of an entry for a BRAF variant.

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Table 1: Number of Associations for Somatic Variants,
Categorized by Clinical Utility
Category

Value

Predictive associations

1800

Prognostic associations

4000

Classification associations

4000

Clinical trial associations

20,000Companion Test—The variant has been identified as a biomarker
correlated to a specific drug, used for treatment of a specific tumor
type. Companion test entries are considered 1 of the highest levels ofevidence in the knowledge base.

Somatic Biomarker Content
The Illumina Knowledge Base currently contains approximately
52,000 potential variant associations with 206 unique drugs, 133diseases, and > 1000 identifiers in the PubMed database (PMIDs).
Predictive variant associations are classified with companion tests,
clinical studies, case reports, and experimental validation levels, with
13 unique companion tests (Table 2). Curated content supporting
predictive variants currently includes:
lllDrug label information curated for FDA-approved drugs, specifying
predictive variants in the disease indication section of drug labels,or as inclusion criteria.
Guidelines for non-small cell lung cancer, breast cancer, coloncancer, rectal cancer, soft tissue sarcoma, melanoma, anddermatofibrosarcoma protuberans, including treatment
recommendations and specified tests for relevant variants.
In collaboration with the American Society of Clinical Oncology(ASCO), the Targeted Agent and Profiling Utilization Registry Study(TAPUR) 4 curates information about 15 targeted anticancer drugs(cetuximab, erlotinib, vemurafenib, crizotinib, dasatinib, adotrastuzumab emtansine, sunitinib, temsirolimus, palbociclib,bosutinib, vismodegib, axitinib, olaparib, regorafenib, andpembrolizumab). Evidence has been sourced from PMID-indexedstudies to identify variants associated with resistance or sensitivity
to each drug.

The Actionable Genome Consortium5 compiled a subset of clinical
trials that were added to the Illumina Knowledge Base. All trials
relevant to biomarkers were manually curated, and were last updatedon June 1, 2015 (Table 2).
Table 2: Number of Associations for Predictive Variants, Basedon Clinical Utility
Category

Target Region/Sequence (Exon)Unique
Associations

Companion test

299

13

Clinical trials

40,600180

Clinical studies

1334

Case reports

167

Experimental

357

Clinical Studies—Cohort analysis is used to determine the potential
role of the variant in predicting tumor response to drug treatment orassociation with outcome endpoints. Studies are included in thedatabase only when statistically significant results between cohorts arereported. Results have not been validated by a regulatory authority.
Case Reports—Published results for individual patients canindicate potential variant associations with treatment outcomes, suchas partial response. Alternatively, case series are also included when apaper identifies a variant associated with response, or lack of response,
to a drug in a subset of tumors. Results have not been validated by aregulatory authority, nor analyzed within a statistically significant study.
Experimental—Published studies that examine variant associations
with the response to a drug treatment within the context of tissue
culture ( in vitro) or animal models ( in vivo) are considered experimental.

Germline Biomarker Curation Process
Germline mutations are heritable genetic alterations found in germline
tissue. These mutations are responsible for genetic diseases
including some types of cancer and rare undiagnosed genetic
disorders. Significance of germline alterations is obtained frompublications and public databases. Disease prevalence and mode ofinheritance are also included for each germline variant association.
Pathogenicity assertions for variant–disease associations are basedon collective evidence following American College of Medical
Genetics and Genomics (ACMG) guidelines published in 2015.9
Interpretations are standardized for optimal readability, summarizing
the collective evidence used to determine pathogenicity. Evidence
supporting the interpretation can be obtained from a variety ofsources, including PubMed. This detailed section also provides
scope, study design, and relevant statistics when available.

Germline Biomarker Content
There are approximately 34,578 germline variants currently present in
the Illumina Knowledge Base, representing 1663 unique diseases
and > 1000 PMID indexes. Curated biomarkers represent a total of> 800 genes (Table 3), with 95% of variants from the 6 ACMG genes( CFTR, MSH2, NF2, LDLR, PMS2, and PCSK9) that were curated inearly 2015.

Evidence Types
Different types of evidence can substantiate an association betweenvariants and utility. Evidence supporting an interpretation can beobtained from various sources, such as PubMed, FDA, and clinical
trial websites.6-8 The Illumina Knowledge Base ranks evidence types
based on credibility and significance of the source of evidence.

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Table 3: Associations for Germline Variant Categorizedby Pathogenicity
Pathogenicity Level

No. ofAssociations

Pathogenic

1129

Likely pathogenic

1682

Variant of unknown significance, suspicious

2154

Variant of unknown significance23,637

Likely benign

1620

Benign4356

ClinVar: Resource for Aggregation and Variant
Interpretation Reports
ClinVar is a public repository of clinically relevant variants, funded by
the National Institutes of Health.1 The ClinVar database contains over
100,000 clinically significant variant–phenotype associations. When
any organization submits a record to ClinVar, the record is assigned asubmitted clinical variant ID (SCV). The SCV record consists of agenomic variant and a clinical phenotype (disease) with comments
and evidence supporting the relationship between variant andphenotype. After review, the ClinVar team assigns a reference clinicalvariant ID (RCV) to an SCV. Additional SCVs with unique identifiers
can be added to existing RCVs, and the RCV may apply to 1 or more
SCV records with equivalent variants and phenotypes. The ClinVar
team adds additional features to the RCV record, such as review
status and phenotype/variant normalization.
ClinVar content is available in BaseSpace Variant Interpreter (Beta) asa source of content on the BaseSpace Knowledge Network (Figure4). Original submissions are displayed at the SCV level, and parsed
from XML and VCF files available on the ClinVar FTP site.10 Variant
submissions with incomplete or misannotated information are filteredout and variants are further validated using the Illumina Annotation
Engine 1.4.1. Data are limited to germline variants for the first releaseof BaseSpace Knowledge Network.
The following fields are parsed for ClinVar variants: Variant, RCV ID,SCV ID, name of submitter, date of submission, date of update, modeof inheritance, level of confidence, phenotype ontology term,ontology ID, and review status (SupplementaryTable 4/1). Because
each SCV may have multiple components with different evidence
types, they are mapped and aggregated into the knowledge network
data model.

Figure 4: Process for Ingestion of ClinVar Version—Multiple SCVs may be a part ofa single RCV and filtered at the RCV or SCV level.

Summary
BaseSpace Variant Interpreter (Beta) and BaseSpace Knowledge
Network are software platforms that reduce time and effort required totransform genomic information into biological insight. The
BaseSpace Knowledge Network curates variant information fromnumerous databases and organizes clinically relevant associations
into an easily accessible and readable interface. The simple userfriendly interface of BaseSpace Variant Interpreter (Beta) integrates
with BaseSpace Knowledge Network, delivering an intuitive
framework for nonexpert users to annotate, filter, and interpret variant
data easily. Together these tools provide a flexible, reliable, andefficient method for enriching variant information with biologicalcontext.

Learn MoreTo learn more about BaseSpace Variant Interpreter (Beta) andBaseSpace Knowledge Network, visit
www.illumina.com/informatics/research/biological-datainterpretation/variant-interpreter.html

References
1.

ClinVar. www.ncbi.nlm.nih.gov/clinvar. Accessed August 3, 2016.

2.

Systematized Nomenclature of Medicine-Clinical Terms.
bioportal.bioontology.org/ontologies/SNOMEDCT. Accessed August 3,
2016.

3.

US National Library of Medicine: Medical Subject Headings.
www.nlm.nih.gov/mesh/. Accessed August 3, 2016.

4.

The Targeted Agent and Profiling Utilization Registry (TAPUR) Study.
www.tapur.org/. Accessed August 3, 2016.

For Research Use Only. Not for use in diagnostic procedures.

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5.

Actionable Genome Consortium to guide NGS in cancer. NatureBiotechnology. 2014;32:965. doi:10.1038/nbt1014-965d. Accessed August
3, 2016.
6.

PubMed. www.ncbi.nlm.nih.gov/pubmed. Accessed August 3, 2016.7.

7.

US Food and Drug Administration. www.fda.gov/default.htm. Accessed
August 3, 2016.

8.

Clinical Trials Database. clinicaltrials.gov/. Accessed August 3, 2016.

9.

Hampel H, Bennett RL, Buchanan A, et al. A practice guideline from theAmerican College of Medical Genetics and Genomics and the National
Society of Genetic Counselors: referral indications for cancer predispositionassessment. Genet Med. 2015;17(1):70-87.

10. ClinVar FTP site. ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/. Accessed August 3,
2016.

Table 4: ClinVar XML Root Paths
ClinVar Extraction Root Path

User Interface Display

ReleaseSet/clinvarset/

Evidence summary,clinvarassertion/observedin/observeddata

PMID

ReleaseSet/clinvarset/clinvarassertion/observedin/sample/originReleaseSet/clinvarset/clinvarassertion/clinicalsignificance/comment
ReleaseSet/clinvarset/clinvarassertion
clinicalsignificance/description
ReleaseSet/clinvarset/ClinVarAssertion/
ClinicalSignificance/ReviewStatus
ReleaseSet/clinvarset/referenceclinvarassertion/
attributeset/attribute
ReleaseSet/clinvarset/ClinVarAssertion/
TraitSet
ReleaseSet/clinvarset/ClinVarAssertion/
ClinVarSubmissionID
ReleaseSet/clinvarset/ReferenceClinVarAssertion/
ClinVarAccession
ReleaseSet/clinvarset/ClinVarAssertion/
ClinVarAccession
ReleaseSet/clinvarset/referenceclinvarassertion/measureset/name/elementvalue
ReleaseSet/clinvarset/ClinVarAssertion/
ClinVarSubmissionID
ReleaseSet/clinvarset/ClinVarAssertion/
ClinVarAccession

ExampleFields et al. (2002) demonstrated that the Fin(major) USH3A mutationin exon 3 of the USH3A gene, which had been identified by Joensuu etal. (2001) as 300C-T (TYR100TER), should be referred to as 528T-G,resulting in a tyr176-to-ter substitution. Joensuu et al. (2001) had
identified homozygosity for this mutation in a Finnish family segregating
Usher syndrome type IIIA (USH3A; 276902) and found it in a further 52
Finnish patients. Fields et al. (2002) found this mutation in 11 of 28
mutated alleles from affected individuals of Finnish and other northern
European ancestry.

Not displayed

Germline

Curator summary

The study set was not selected for affection status in relation to anycancer. Pathogenicity categories were based on literature curation.
See PubMed ID:22703879 for details.

Pathogenicity

Uncertain significance

Review status

Reviewed by expert panel

Mode of inheritance

Autosomal recessive inheritancePhenotype

Usher syndrome, type 3

Submitted byOMIM

RCV

RCV000004642.1

SCV

SCV000024816.1

Not displayed, used to join on IAE

NM_001195794.1:c.567T>G

Submitted date"2015-01-29"

Updated date"2015-01-30"

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see www.illumina.com/company/legal.html. Pub. No. 970-2016-023-A QB #For Research Use Only. Not for use in diagnostic procedures.

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