ANATOMICAL MOLECULAR LABORATORY

Introduction

The Anatomical Molecular Laboratory (ATOM) (former Translational Pathology Centre or TPC) is a molecular laboratory under the Department of Anatomical Pathology. It offers a variety of tests for molecular profiling of various cancers / tumours, either on tumour tissue or on cell-free nucleic acids in the peripheral blood (liquid biopsy).

ATOM currently offers the following clinical tests:

The test menu will be progressively expanded over time.

Somatic Solid Tumour Panel (SSTP) assay

The SSTP assay is a small panel amplicon-based next generation sequencing (NGS) assay that can detect single nucleotide variants (SNVs) and short insertion/deletions (delins) in 15 to 18 genes. It can be used for mutational testing of lung cancers, colorectal cancers, gastrointestinal stromal tumours (GISTs), melanomas and other solid tumours where the genomic alterations covered by the assay is relevant. It does not cover copy number variations (CNVs), gene fusions or other genomic alterations.

While the assay is subdivided into Lung, Colon and GIST / Melanoma panels for these tumour types, other tumour types can also be tested using any of these panels as long as the relevant genes of interest are covered. For example, mutational testing for PIK3CA, AKT1 and PTEN in breast cancers or IDH1, IDH2 and BRAF in brain tumours can be performed using the SSTP Lung panel as these genes are included in the panel. Similarly, POLE testing for endometrial cancers can also be performed using the SSTP Lung panel as it covers the POLE gene.

The list of genes, specimen requirements and other details of the assay can be found in the link below:

Click here to view more details on SSTP assay

Somatic Solid Tumour Liquid Panel (SSTP Liquid) assay

The SSTP Liquid assay is an amplicon-based next generation sequencing (NGS) assay incorporated with molecular tagging that allows sensitive detection of circulating cell-free tumour nucleic acids in the peripheral blood (liquid biopsy). This assay can be used to determine the presence of genomic alterations in circulating tumour nucleic acids in patients that would predict response of a cancer to targeted therapy (predictive testing).

The list of genes, specimen requirements and other details of the assay can be found in the link below:

Click here to view more details on SSTP Liquid assay

Click here to view CPOE ordering instructions for SSTP Liquid (for relevant SingHealth institutions)

Somatic Solid Tumour Comprehensive Panel (SSTP Comprehensive) assay

The SSTP Comprehensive Assay is a targeted panel NGS assay that simultaneously analyses both DNA and RNA in one integrated workflow. The panel detects multiple variant types and biomarkers across 523 cancer-relevant genes from DNA and 55 genes from RNA. Library preparation is based on hybrid–capture chemistry with unique molecular identifiers (UMIs) added for error correction to achieve high analytical specificity.

The DNA workflow allows detection of single nucleotide variants and small insertions / deletions in 523 genes and copy number variant detection in 514 genes. It also allows assessment of microsatellite instability (MSI) and tumour mutational burden (TMB). When the homologous recombination repair deficiency (HRD) workflow is added, a Genomic Instability Score (GIS) can be calculated, powered by Myriad Genetics. The RNA workflow allows detection of gene fusions in 55 genes of which 3 are also tested for RNA exon splice variants.

The list of genes, specimen requirements and other details of the assay can be found in the link below:

Click here to view more details on the SSTP Comprehensive assay

TCRB + TCRG T-cell clonality assay and IGH + IGK B-cell clonality assay

The T-cell and B-cell clonality assays are PCR-based assays that use multiple consensus DNA primers in a multiplex fashion, targeting the conserved genetic regions within the T-cell receptor beta (TCRB) and gamma (TCRG) genes and the immunoglobulin heavy (IGH) and kappa light chain (IGK) genes respectively. The presence of a clonal gene rearrangement product can help confirm the presence of a lymphoid malignancy in a lesion with concordant clinical, histological and immunophenotypic features.

Click here to view more details on TCRB + TCRG T-cell clonality assay and IGH + IGK B-cell clonality assay

Specimen Request Form Requirements for All Specimens

All specimens are to be accompanied by a hard copy test request form or an electronic test request order in the Computerised Physician Order Entry system (CPOE) (for relevant SingHealth institutions). The hard copy request form or CPOE order should include the following information:

Patient's name, NRIC/passport number, visit account number, age, sex, date of birth
Hospital, department and ward number, or name of clinic with telephone / fax number
Clinical Diagnosis (including primary site of cancer)
Clinical History / relevant clinical information, including any previous treatment rendered
Nature of specimen (including paraffin block number for tissue specimens), nature of procedure/operation, anatomical site, and date and time specimen was taken
Name of consultant-in-charge / doctor performing procedure, their MCR number and telephone number

Translational / Research Work

Besides clinical testing, the laboratory has other capabilities that are used in the translational / research space:

DNA / RNA extraction
PCR based assays
Sanger sequencing
Digital droplet PCR
Next generation sequencing

Laboratory Operating Hours & Contact Details

Monday – Friday: 8.30am – 5.30pm

Address: 20 College Road, Academia building, Ngee Ann Kongsi Discovery Tower Level 10, Anatomical Molecular Laboratory (ATOM), Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856

Telephone: (65) 6576 7191

Fax: (65) 6227 6562