ISO15189 accreditation to deliver clinical genomics to pathology providers

With expertise in Next Generation Sequencing technologies and clinical bioinformatics, AGRF delivers innovative, robust and reproducible clinical genomics services with the sensitivity needed to meet NATA and NPAAC requirements.

With a strong focus on sample traceability, integrity, and accuracy, we have benchmarked our variant calling pipeline both nationally and internationally.

Our expertise, coupled with a suite of sequencing platforms, enables AGRF to tailor tests to the needs of our clinical partners.

We contribute our specialist expertise and resources to the national healthcare agenda through our membership and partnerships with national and state genomics health alliances.

Whole Exome Sequencing

Whole exome sequencing (WES) is a powerful tool for investigation of genetic variance across the protein coding regions of the genome, providing high coverage and high confidence in variant calls for the study of rare mendelian disorders, complex diseases and cancer.

AGRF provides comprehensive solutions for WES, including bioinformatics using gold standard tools (Illumina DRAGEN).

Our Clinical WES Service

• ISO15189 Accreditation to deliver secondary analysis to our clinical pathology partners

• Illumina Sequencing: 150bp paired end reads

• Mapped coverage: 30x

• Twist Exome v2

• Twist Alliance Clinical Research Exome

• Germline variant calling

Options for Translational Research

• Twist Comprehensive v2 Human WES – Standard Research • Twist Comprehensive Exome V2 (36 Mbp Target) • Illumina Sequencing – 150bp paired end reads, with a minimum 5 Gbp and mean on-target coverage 40-80x 

• Twist Comprehensive v2 Human WES – Deep Research • Twist Comprehensive Exome V2 (36 Mbp Target) • Illumina Sequencing – 150bp paired end reads, with a minimum 10Gbp and mean on-target coverage 80-160x

For more information, go to our Whole Exome Sequencing Service Guide.

Whole Genome Sequencing

Whole genome sequencing (WGS) provides the most comprehensive analysis of genome variance and structure. WGS enables accurate detection of single nucleotide variants (SNV), and structural variation of human genomes, or de novo assembly and variant detection of non-human genomes. AGRF offers a range of services for sequencing of small microbial genomes, large complex genomes and a clinical genome sequencing service for rare mendelian disorders, complex disease and cancer.

Complex Disease Studies Pharmacogenomics Research Lifestyle & Wellness Characterisation

Illumina’s Global Screening Array (GSA) contains 654,027 markers, of which 45,998 are ClinVar pathogenic and ClinVar likely pathogenic. The array also contains 301,888 markers for COSMIC genes for Somatic mutations in cancer. The array can be used for pharmacogenomic applications and has 4,125 markers for PharmGKB which have applications in human genetic variation associated with drug responses.

Optional content for GSA include:

• GSA Multi-Disease Drop-In Panel: With approximately 50,000 markers, the Multi-Disease Drop-In Panel provides fine-mapping of content derived from exome sequencing and meta-analysis of phenotype-specific consortia focused on the following traits: psychiatric, neurological, cancer, cardiometabolic, autoimmune, and anthropometric.

• GSA PsychArray: The PsychArray24 focused content panel features approximately 30,000 markers associated with common psychiatric disorders including: schizophrenia, bipolar disorder, autism spectrum disorders, attention defi cit hyperactivity disorder, major depressive disorders, obsessive compulsive disorder, anorexia, and Tourette’s syndrome.

Constitutional Cytogenetics

The identification of structural chromosomal aberrations can provide insight into causative relationships with complex phenotypes - including intellectual disability, developmental delay, and congenital anomalies.

AGRF uses Illumina’s HumanCytoSNP-12 and CytoSNP-850k BeadChip cytogenetic microarrays to reliably detect chromosomal imbalances of copy number and allelic homozygosity, which are commonly associated with genetic constitutional disorders.

Coverage for Clinical Applications

• Analytical sensitivity for detection of low-level mosaics

• Reproducible data with challenging samples, including FFPE

• Simple workflows using the proven Infinium assay chemistry for confident results

Translational Research for Complex Disease

AGRF provides the option of using the Illumina MethylationEPIC array to characterise complex diseases and for tumour classification.

EPIC Array differentiaties >80 sub-entities in central nervous system tumours and approximately 60 sub-entities in sarcoma, as well as classifying epithelial cancer tumours.

Clinical Variant Confirmation

Next generation sequencing (NGS) technologies and the advent of whole exome, whole genome and genome-wide sequencing has significantly improved the detection of clinically relevant genetic variants. With this comes the need to confirm the presence of variants of diagnostic importance. Sanger sequencing is widely considered the gold standard technology for DNA sequence analysis and is therefore ideal for confirming variant calls made on NGS platforms.

AGRF’s clinical variant confirmation service can provide confirmation of any variant using Sanger sequencing. Simply provide the genomic coordinates of your variant/s and submit your purified genomic DNA. We will design and order primers, amplify and sequence the variant. Data is supplied for your interpretation and diagnostic reporting.

Why confirm a variant?

A recent study has shown 1.3% of variants detected by NGS can be false-positives*. These are often the result of complex genomic regions such as homopolymer stretches and GC or AT rich regions (65%) which can cause low coverage or poor mapping. Sanger sequencing can confi rm the presence of the variant with high specifi city. Variants can be confi rmed in a single individual or as a trio. A trio is required for cascade testing and usually consists of either the patient plus their parents, or the patient plus their children.

*Mu W, Lu H-M, Chen J, Li S, Elliott AM. Sanger confirmation is required to achieve optimal sensitivity and specifi city in next-generation sequencing panel testing. The Journal of Molecular Diagnostics. November 2016 18(6):923-32.