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The most efficient
HRD test for
Ovarian cancer

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The most efficient HRD test for Ovarian Cancer

Ovarian cancer is the third most common gynecological cancer in Indian women.

Ovarian cancer has the worst prognosis amongst gynecological cancers with a 5 year survival rate of 45%.

This is primarily because, most often ovarian cancer is diagnosed at advanced stages (stage III or IV). The primary treatment approach is a combination of surgical tumor removal and platinum-based chemotherapy.

Advanced types of high grade serous ovarian cancer are characterized by genomic instability due to homologous recombination deficiency (HRD) which causes characteristic genomic scars due to low-fidelity DNA repair mechanisms

About 1 in 4 women with advanced ovarian cancer has a BRCA mutation and 1 in 2 women are HRD positive.

  • In the human body, the primary mechanism of repairing DNA double-strand breaks is Homologous Recombination Repair (HRR).
  • The most prominent genes involved in Homologous Recombination Repair are BRCA1 and BRCA2 along with other genes such as RAD51, ATM/ATR, CDK12 -complex, etc.
  • When the functionality of these genes are lost, it results in DNA double strand breaks, which persists and causes complete damage of DNA at that site, and subsequent repair by nonhomologous end-joining, a low-fidelity repair pathway that introduces inversions and other genomic aberrations.
  • This functional defects in Homologous Recombination Repair mechanisms is known as Homologous Recombination Deficiency (HRD).
  • Up to 50% of women with advanced ovarian cancer have HRD positive cancer cells.
  • Patients who are HRD positive respond well to PARPi (poly ADP-ribose inhibitors), a relatively new targeted frontline therapy.
  • Determining HRD status leads to selection of more patients who benefit from PARPi therapy.
  • Besides ovarian cancer, HRD may be found in other cancers, including breast, pancreatic and prostate cancer.
Homologous Recombination
Repair test (HRR test)

HRR testing analyzes mutations in homologous recombination repair genes

Assist in identifying potential therapeutic options and inform risks for other cancers

It is an NGS based test to identify deleterious/ suspected deleterious somatic and germline mutations in a single assay

The mutations in HRR are commonly investigated in the genes BRCA1, BRCA2, ATM, CDK12, CHEK1, CHEK2, FANCL, PALB2, BRIP1, RAD51B, RAD51C,BARD1, RAD51D, and RAD54L, PPP2R2A

Detects variants in HRR genes

Homologous Recombination
Deficiency test (HRR test)

HRD testing is used to assess the genomic instability status & the tumor BRCA1/BRCA2 mutation status in genomic DNA

Aid to determine extend of benefit from treatment with PARP inhibitors

It is NGS based test to detect single nucleotide variants, insertions & deletions , large rearrangements in BRCA1/BRCA2 variants in thosands of loci across the genome

HRD testing assess BRCA1/BRCA2 mutation status and evaluates a genomic scar score based on different copy number changes

Determines HRD status by detecting BRCA mutations and an algorithmic computation of genomic instability as a GSS (Genomic Scar Score)

Proof-product-1

~50% patients in the PAOLA-1 trial were HRD positive

 

HRD testing can detect mutations in BRCA1 and BRCA2 genes and computes a genomic scar score to evaluate HRD status. it can help to

HRD Test Description

HRD status is analyzed by identifying mutations in BRCA1 and BRCA2 genes and by calculating a genomic scar score (GSS)
HRD assessment is an important prognostic and predictive biomarker in breast and ovarian cancers
HRD testing is an NGS (next generation sequencing) based diagnostic test
Strand HRD assesses single nucleotide variants, insertions and deletions, in whole coding regions and intron/exon boundaries of the BRCA1 and BRCA2 genes
Determines the Genomic Scar Score (GSS) as a weighted sum of copy number variations through a machinelearning based model trained on breast and ovarian cancer samples
Homologous Recombination
Repair test (HRR test)

HRR testing analyzes mutations in homologous recombination repair genes

Assist in identifying potential therapeutic options and inform risks for other cancers

It is an NGS based test to identify deleterious/ suspected deleterious somatic and germline mutations in a single assay

The mutations in HRR are commonly investigated in the genes BRCA1, BRCA2, ATM, CDK12, CHEK1, CHEK2, FANCL, PALB2, BRIP1, RAD51B, RAD51C,BARD1, RAD51D, and RAD54L, PPP2R2A

Detects variants in HRR genes

Homologous Recombination
Deficiency test (HRR test)

HRD testing is used to assess the genomic instability status & the tumor BRCA1/BRCA2 mutation status in genomic DNA

Aid to determine extend of benefit from treatment with PARP inhibitors

It is NGS based test to detect single nucleotide variants, insertions & deletions , large rearrangements in BRCA1/BRCA2 variants in thosands of loci across the genome

HRD testing assess BRCA1/BRCA2 mutation status and evaluates a genomic scar score based on different copy number changes

Determines HRD status by detecting BRCA mutations and an algorithmic computation of genomic instability as a GSS (Genomic Scar Score)

Proof-product-1

HRD testing can detect mutations in BRCA1 and BRCA2 genes and computes a genomic scar score to evaluate HRD status. it can help to

HRD Test Description

GET A CALLBACK
HRD status is analyzed by identifying mutations in BRCA1 and BRCA2 genes and by calculating a genomic scar score (GSS)
HRD assessment is an important prognostic and predictive biomarker in breast and ovarian cancers
HRD testing is an NGS (next generation sequencing) based diagnostic test
Strand HRD assesses single nucleotide variants, insertions and deletions, in whole coding regions and intron/exon boundaries of the BRCA1 and BRCA2 genes
Determines the Genomic Scar Score (GSS) as a weighted sum of copy number variations through a machinelearning based model trained on breast and ovarian cancer samples

Strand HRD is based on the HANDLE System: Halo-shape Annealing and Defer-Ligation Enrichment System, an Improved Molecular Inversion Probe (MIP) technology:




HRD status is analyzed by identifying mutations in BRCA1 and BRCA2 genes and by calculating a genomic scar score (GSS)
HRD assessment is an important prognostic and predictive biomarker in breast and ovarian cancers
HRD testing is an NGS (next generation sequencing) based diagnostic test
Strand HRD assesses single nucleotide variants, insertions and deletions, in whole coding regions and intron/exon boundaries of the BRCA1 and BRCA2 genes
Determines the Genomic Scar Score (GSS) as a weighted sum of copy number variations through a machinelearning based model trained on breast and ovarian cancer samples

Strand HRD is based on the HANDLE System: Halo-shape Annealing and Defer-Ligation Enrichment System, an Improved Molecular Inversion Probe (MIP) technology:

Test Requirements

Sample Requirements
Formalin-Fixed Paraffin-Embedded (FFPE) tissue specimens with TMB>=30%

TAT

  21 Days for the receipt of sample

FAQs

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What is HRD Status ?

Homologous recombination (HR) is the way our body fixes damaged DNA. When homologous recombination is not able to fix damaged DNA, this is called homologous recombination deficiency (HRD). Approximately 50% of all ovarian cancer tumors have homologous recombination deficiency. Your HRD status will be determined one of two ways, first by analyzing for a change in your BRCA1 and BRCA2 genes, and second through a specialized tool known as genomic instability.

What does HRD Status Mean to You?

If you are found to be HRD+, your tumor is more likely to respond to a type of drug called a PARP inhibitor than those tumors that are not HRD+. These ovarian tumors are more likely to shrink when a PARP inhibitor is used.

What are PARP inhibitors?

PARP inhibitors, or poly (ADP-ribose) polymerase inhibitors, are pills that are taken by mouth after being prescribed to you by a physician. They may be used to treat women with ovarian cancer. PARP inhibitors work by blocking DNA from being repaired. If the DNA damage cannot be repaired, the cancer cell will be killed. If a cancer cell is like a balloon, a PARP inhibitor is like the needle trying to pop it.

What is the Strand HRD test?

It is a "Genomic Instability Score Card" , which helps physicians take informed decison on treatment methods for cancers, especially ovarian cancer. Chromosomal instability leads to Genomic Scars which affects the body's DNA Repair mechanism (HRR) with gene mutation. The Strand HRD Panel checks if a patient is HRD positive (they have deficiency in DNA repair mechanism). If found positive, it helps clinicians propose a therapy - PARP (poly ADP-ribose) inhibitors - a relatively new targeted frontline therapy as a potential approach with higher rates of success. Thus, determining HRD Status leads to more positive outcomes for people diagnosed with Ovarian Cancers The Strand HRD test is an NGS test that sequences BRCA1/2 genes and tens of thousands of loci across the genome. The BRCA 1/2 gene regions are analyzed for the presence of pathogenic and likely pathogenic mutations. The genome wide data is used to compute a Genomic Scar Score (GSS) which is a measure of genomic instability. The sequencing is carried out on the Illumina NextSeq platform

What information does the Strand HRD test provide?

The Strand HRD test identifies pathogenic/likely pathogenic mutations in the BRCA 1/2 genes. It also computes a Genomic Scar Score (GSS) which is a measure of genomic instability status. The presence of BRCA mutations and the GSS are used to assign a HRD status to a sample. Patients who are HRD positive (HRD+) are likely to benefit from PARPi treatments.

How is the Strand HRD Genomic Instability Status calculated?

The Genomic Instability Status (GIS) is computed by sequencing loci across tens of thousands of regions spread across the genome. The sequencing data is used to segment the genome into regions with varying heterozygosity and copy number status. The length and locations of the aberrant genomic regions are all summarized into a single metric.

What is the Strand HRD threshold used to define GIS positivity or negativity?

Samples with GSS >= 50 are classified as GIS positive or GIS high. A GSS value < 50 is considered GIS negative or GIS low.

What information is provided in the Strand HRD test report?

The Strand HRD report indicates the pathogenic or likely pathogenic mutations (if any) detected in the sample. It also indicates if the genomic instability is high or low. And finally, it labels samples as HRD positive or negative based on the mutations and the level of genomic instability.

Is the Genomic Instability Status provided as a number or just as positive or negative?

The Genomic Instability Status (GIS) value is indicated as Low /High. The Genomic Scar Score (GSS) is a numerical measure of genomic instability.

Could a patient with a VUS in either BRCA1 or BRCA2 genes still be HRD+?

Yes. A sample is classified as HRD+ if pathogenic /likely pathogenic mutations are detected in BRCA 1 /2 genes or if the sample has high genomic instability. So, samples without mutations but with high genomic instability will be called HRD+.

Will the GIS vary if a VUS in BRCA gene is then reclassified as at a later stage?

No. The GIS is independent of the BRCA mutations. GIS is based on tens of thousands of loci across the genome and is not dependent on BRCA mutation status. However, a sample with low GIS can be reclassified as HRD+ if the mutation classification changes from VUS to pathogenic /likely pathogenic.

PAOLA1 trial showed inconclusive results (11.3% cases), how can inconclusive results be avoided?

FFPE samples which fail library preparation, or which perform poorly in sequencing can result in inconclusive results. The age of the block, poor fixation processes, and small amounts of tissue can all lead to sample failures. Samples with less than 30% tumor content also cannot be processed.

Is there a Customer Service Number available should the HCP need information on the Strand HRD Result Report?

The HCP can reach out to Strand at +91 6366937263 or send an email to hello@strandls.com for any information regarding the HRD Result Report.

What type of sample is needed for the Strand HRD test? Are unstained slides acceptable samples?

The preferred sample type is an FFPE specimen with tumor content> 30%. The block should yield a minimum of 100ng of DNA with DIN (DNA integrity number) > 3, and should not be more than 1 year old. Slides are not acceptable at present.

Is it possible to use blood or saliva samples to determine Strand HRD score?

No. Blood or saliva samples only carry trace amounts of tumor derived DNA (< 5% ). The Strand HRD test requires DNA with a minimum of 30% tumor content.

Will remaining tumor samples be sent to the pathology lab?
The threshold for labeling a sample as having high genomic instability is 50.
What is the definition of LCN, TCN, SCN? How does LCN+TCN+SCN different LOH+TAI+LST?

LCN refers to the length of the copy number event. Events are termed as Large (> 15Mbp), Medium (10-15Mbp) or Small(5-10Mbp). TCN refers to the type of the copy number event which can be LOH, Balanced copy number change or other. SCN refers to the site of copy number change - telomere, centromere or other. GSS is a weighted function of LCN, TCN, SCN. Whereas LOH+TAI+LST is an unweighted sum of the events. The underlying detection of copy number aberrant regions is similar. However, the score is derived differently in the two cases.

Is there a sample Strand HRD test report and TRF ?
  • Dummy report: Negative
  • Dummy report: Positive
How does the team validate the Strand HRD test?

An analytical control was sequenced in multiple runs to evaluate reproducibility of mutation calling and GSS score computation. Another mutation positive analytical control specifically designed to contain BRCA mutations in the 5-10% allele frequency range was sequenced to ensure that somatic mutations could be called accurately in the BRCA genes. Multiple clinical samples with known BRCA mutations were sequenced to assess the accuracy of mutation detection. Several clinical samples were sequenced using an alternate whole genome sequencing approach to ensure accuracy of the genomic instability metric.

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FAQs

Share on whatsapp
Chat Now
What is HRD Status ?
Homologous recombination (HR) is the way our body fixes damaged DNA. When homologous recombination is not able to fix damaged DNA, this is called homologous recombination deficiency (HRD). Approximately 50% of all ovarian cancer tumors have homologous recombination deficiency. Your HRD status will be determined one of two ways, first by analyzing for a change in your BRCA1 and BRCA2 genes, and second through a specialized tool known as genomic instability.
What does HRD Status Mean to You?
If you are found to be HRD+, your tumor is more likely to respond to a type of drug called a PARP inhibitor than those tumors that are not HRD+. These ovarian tumors are more likely to shrink when a PARP inhibitor is used.
What are PARP inhibitors?
PARP inhibitors, or poly (ADP-ribose) polymerase inhibitors, are pills that are taken by mouth after being prescribed to you by a physician. They may be used to treat women with ovarian cancer. PARP inhibitors work by blocking DNA from being repaired. If the DNA damage cannot be repaired, the cancer cell will be killed. If a cancer cell is like a balloon, a PARP inhibitor is like the needle trying to pop it.
What is the Strand HRD test?
It is a "Genomic Instability Score Card" , which helps physicians take informed decison on treatment methods for cancers, especially ovarian cancer. Chromosomal instability leads to Genomic Scars which affects the body's DNA Repair mechanism (HRR) with gene mutation. The Strand HRD Panel checks if a patient is HRD positive (they have deficiency in DNA repair mechanism). If found positive, it helps clinicians propose a therapy - PARP (poly ADP-ribose) inhibitors - a relatively new targeted frontline therapy as a potential approach with higher rates of success. Thus, determining HRD Status leads to more positive outcomes for people diagnosed with Ovarian Cancers
What information does the Strand HRD test provide?
The Strand HRD test identifies pathogenic/likely pathogenic mutations in the BRCA 1/2 genes. It also computes a Genomic Scar Score (GSS) which is a measure of genomic instability status. The presence of BRCA mutations and the GSS are used to assign a HRD status to a sample. Patients who are HRD positive (HRD+) are likely to benefit from PARPi treatments.
How is the Strand HRD Genomic Instability Status calculated?
The Genomic Instability Status (GIS) is computed by sequencing loci across tens of thousands of regions spread across the genome. The sequencing data is used to segment the genome into regions with varying heterozygosity and copy number status. The length and locations of the aberrant genomic regions are all summarized into a single metric.
What is the Strand HRD threshold used to define GIS positivity or negativity?
Samples with GSS >= 50 are classified as GIS positive or GIS high. A GSS value < 50 is considered GIS negative or GIS low.
What information is provided in the Strand HRD test report?
The Strand HRD report indicates the pathogenic or likely pathogenic mutations (if any) detected in the sample. It also indicates if the genomic instability is high or low. And finally, it labels samples as HRD positive or negative based on the mutations and the level of genomic instability.
Is the Genomic Instability Status provided as a number or just as positive or negative?
The Genomic Instability Status (GIS) value is indicated as Low /High. The Genomic Scar Score (GSS) is a numerical measure of genomic instability.
Could a patient with a VUS in either BRCA1 or BRCA2 genes still be HRD+?
Yes. A sample is classified as HRD+ if pathogenic /likely pathogenic mutations are detected in BRCA 1 /2 genes or if the sample has high genomic instability. So, samples without mutations but with high genomic instability will be called HRD+.
Will the GIS vary if a VUS in BRCA gene is then reclassified as at a later stage?
No. The GIS is independent of the BRCA mutations. GIS is based on tens of thousands of loci across the genome and is not dependent on BRCA mutation status. However, a sample with low GIS can be reclassified as HRD+ if the mutation classification changes from VUS to pathogenic /likely pathogenic.
PAOLA1 trial showed inconclusive results (11.3% cases), how can inconclusive results be avoided?
FFPE samples which fail library preparation, or which perform poorly in sequencing can result in inconclusive results. The age of the block, poor fixation processes, and small amounts of tissue can all lead to sample failures. Samples with less than 30% tumor content also cannot be processed.
Is there a Customer Service Number available should the HCP need information on the Strand HRD Result Report?
The HCP can reach out to Strand at +91 6366937263 or send an email to hello@strandls.com for any information regarding the HRD Result Report.
What type of sample is needed for the Strand HRD test? Are unstained slides acceptable samples?
The preferred sample type is an FFPE specimen with tumor content> 30%. The block should yield a minimum of 100ng of DNA with DIN (DNA integrity number) > 3, and should not be more than 1 year old. Slides are not acceptable at present.
Is it possible to use blood or saliva samples to determine Strand HRD score?
No. Blood or saliva samples only carry trace amounts of tumor derived DNA (< 5% ). The Strand HRD test requires DNA with a minimum of 30% tumor content.
Will remaining tumor samples be sent to the pathology lab?
The threshold for labeling a sample as having high genomic instability is 50.
What is the definition of LCN, TCN, SCN? How does LCN+TCN+SCN different LOH+TAI+LST?
LCN refers to the length of the copy number event. Events are termed as Large (> 15Mbp), Medium (10-15Mbp) or Small(5-10Mbp). TCN refers to the type of the copy number event which can be LOH, Balanced copy number change or other. SCN refers to the site of copy number change - telomere, centromere or other. GSS is a weighted function of LCN, TCN, SCN. Whereas LOH+TAI+LST is an unweighted sum of the events. The underlying detection of copy number aberrant regions is similar. However, the score is derived differently in the two cases.
Is there a sample Strand HRD test report and TRF ?
  • Dummy report: Negative
  • Dummy report: Positive
How does the team validate the Strand HRD test?
An analytical control was sequenced in multiple runs to evaluate reproducibility of mutation calling and GSS score computation. Another mutation positive analytical control specifically designed to contain BRCA mutations in the 5-10% allele frequency range was sequenced to ensure that somatic mutations could be called accurately in the BRCA genes. Multiple clinical samples with known BRCA mutations were sequenced to assess the accuracy of mutation detection. Several clinical samples were sequenced using an alternate whole genome sequencing approach to ensure accuracy of the genomic instability metric.
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