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BMC Medical Genomics

, 7:2

Functional and structural genomics

Abstract

BackgroundTo gain biological insights into lung metastases from hepatocellular carcinoma HCC, we compared the whole-genome sequencing profiles of primary HCC and paired lung metastases.

MethodsWe used whole-genome sequencing at 33X-43X coverage to profile somatic mutations in primary HCC HBV+ and metachronous lung metastases > 2 years interval.

ResultsIn total, 5,027-13,961 and 5,275-12,624 somatic single-nucleotide variants SNVs were detected in primary HCC and lung metastases, respectively. Generally, 38.88-78.49% of SNVs detected in metastases were present in primary tumors. We identified 65–221 structural variations SVs in primary tumors and 60–232 SVs in metastases. Comparison of these SVs shows very similar and largely overlapped mutated segments between primary and metastatic tumors. Copy number alterations between primary and metastatic pairs were also found to be closely related. Together, these preservations in genomic profiles from liver primary tumors to metachronous lung metastases indicate that the genomic features during tumorigenesis may be retained during metastasis.

ConclusionsWe found very similar genomic alterations between primary and metastatic tumors, with a few mutations found specifically in lung metastases, which may explain the clinical observation that both primary and metastatic tumors are usually sensitive or resistant to the same systemic treatments.

KeywordsCancer Hepatocellular carcinomas HCC Lung metastasis Somatic Next-generation sequencing NGS AbbreviationsHCCHepatocellular carcinoma

SNVsSingle-nucleotide variants

SVsStructural variations

CNAsCopy number alterations

SSMsSomatic SNV mutations

NGSNext-generation sequencing

TACETranscatheter arterial chemoembolization

COSMICCatalogue of somatic mutations in cancer

ICGCInternational cancer genome consortium

TCGAThe cancer genome atlas

OICROntario institute for cancer research

NCCNational cancer center.

Electronic supplementary materialThe online version of this article doi:10.1186-1755-8794-7-2 contains supplementary material, which is available to authorized users.

Limei Ouyang, Jeeyun Lee, Cheol-Keun Park contributed equally to this work.

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Author: Limei Ouyang - Jeeyun Lee - Cheol-Keun Park - Mao Mao - Yujian Shi - Zhuolin Gong - Hancheng Zheng - Yingrui Li - Yonggang

Source: https://link.springer.com/



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