Cancer Sample 13 Report

Golden Labs
203 Enterprise Blvd
Bozeman, 59715
Phone: 406 587 8137
Fax: 405 555 5555

Provider Information

Physician: Dr. Natalie Amidala
Institution: ACME General Hospital
Case Id: GL-1234

Patient Information

Name: Cancer Sample 13
Gender: Male
Date of Birth: 1/11/2017
Id: 1234

Sample Information

Sample Site: Blood
Sample Type: Blood
Collection Method: Peripheral Draw
Panel Coverage: 99.73%

Avg. Read Depth: 542x
Collection Date: 1/11/2017
Receipt Date: 1/11/2017
Report Date: 1/11/2017

Results

Positive: Mutations with an establish somatic link detected.

Affected Genes

APC

(0)
ATM

(0)
BARD1

(0)
BMPR1A

(0)
BRCA1

(0)
BRCA2

(1)
BRIP1

(0)
CDH1

(0)
CDK4

(0)
CDKN2A

(0)
CHEK2

(0)
EPCAM

(0)
KLLN

(0)
MEN1

(0)
MLH1

(0)
MSH2

(0)
MSH6

(0)
MUTYH

(0)
NBN

(0)
NF1

(0)
PALB2

(0)
PMS2

(0)
POLD1

(0)
POLE

(0)
PTEN

(0)
RAD51C

(0)
RAD51D

(0)
RET

(9)
STK11

(0)
TP53

(0)
VHL

(0)

Primary Findings

Gene	Type	Variant	Exon	Pathogenicity
BRCA2	CNV	4 exon duplication spanning 8,812bp	8-12	Pathogenic
RET	?	NM_020975.4:c.1946C>T(NP_066124.1:p.Ser649Leu)	11	Pathogenic
RET	?	NM_020975.4:c.2071G>A(NP_066124.1:p.Gly691Ser)	11	Pathogenic
RET	?	NM_020975.4:c.2944C>T(NP_066124.1:p.Arg982Cys)	18	Pathogenic
BRCA2	?	NM_000059.3:c.2971A>G(NP_000050.2:p.Asn991Asp)	11	Pathogenic

Interpretation Summary

Recommendations

OncoMD Drug Summary

OncoMD Trial Summary

RET

Cancer Type	Country	Drugs	Inclusion Criterion	Status	Trial Number
Neoplasms	Australia	Sorafenib (Nexavar, BAY43-9006)	RET MUTATION	Recruiting	NCT00625378
Soft Tissue Sarcoma	Australia	Sunitinib malate	RET MUTATION	Recruiting	NCT00753727
Neoplasms	Belgium	Sorafenib (Nexavar, BAY43-9006)	RET MUTATION	Recruiting	NCT00625378
Neoplasms	Brazil	Sorafenib (Nexavar, BAY43-9006)	RET MUTATION	Recruiting	NCT00625378
Hepatocellular Carcinoma	Brunei Darussalam	Sorafenib tosylate	RET MUTATION	Recruiting	NCT01135056
Neoplasms	Canada	Sorafenib (Nexavar, BAY43-9006)	RET MUTATION	Recruiting	NCT00625378
Paraganglioma	Canada	Sunitinib	RET MUTATION	Recruiting	NCT00843037
Kidney Cancer	Canada	sunitinib malate	RET MUTATION	Recruiting	NCT01099423
Hepatocellular Carcinoma	China	Sorafenib tosylate	RET MUTATION	Recruiting	NCT01135056
Hepatectomy	China	sorafenib	RET MUTATION	Recruiting	NCT01409499

Individual Variant Interpretations

NP_066124.1:p.Ser649Leu in Exon 11 of RET (NM_020975.4:c.1946C>T) Pathogenic

NP_066124.1:p.Gly691Ser in Exon 11 of RET (NM_020975.4:c.2071G>A) Pathogenic

NP_066124.1:p.Arg982Cys in Exon 18 of RET (NM_020975.4:c.2944C>T) Pathogenic

NP_000050.2:p.Asn991Asp in Exon 11 of BRCA2 (NM_000059.3:c.2971A>G) Pathogenic

Incidental Findings

NP_066124.1:p.= in Exon 2 of RET (NM_020975.4:c.135A>G)

NP_066124.1:p.Ser220Cys in Exon 4 of RET (NM_020975.4:c.658A>T)

NP_066124.1:p.= in Exon 7 of RET (NM_020975.4:c.1296A>G)

NP_066124.1:p.= in Exon 13 of RET (NM_020975.4:c.2307G>T)

NP_066124.1:p.Ala999Val in Exon 18 of RET (NM_020975.4:c.2996C>T)

References

Test

Illumina TruSight Myeloid Sequencing Panel

Indication

The panel targets 54 tumor suppressor genes and oncogenetic hotspots for somatic mutations in hematological malignancies.

Background

The TruSight Myeloid Sequencing Panel uses next-generation sequencing (NGS) technology to provide a comprehensive assessment of 54 genes (tumor suppressor genes and oncogenetic hotspots) in one test. The panel targets mutations with known involvement in acute myeloid leukemia (AML). Myelodsyplastic syndrome (MDS), myelopriliferative neoplasms (MPN), chronic myelogenous leukemia (CML), and juvenile myelomocylic leukemia (JMML). The result is a single assay for accurate, economical, and rapid profiling of liquid tumors for disease status and prognosis, in multiple samples.

Method

TruSight Myeloid features a highly optimized oligo pool specific for investigating genomic changes associated with hematological malignancies. The panel focuses on ~ 141 kb of genomic content consisting of 568 amplicons of ~ 250 bp in length designed against the human NCB37/mg19 reference genome. The oligo pool targets 15 full genes (exons only) plus exonic hotspots of an additional 39 genes, providing nearly 100% coverages of all targeted regions.

This optimized oligo pool provides uniform coverage of the target regions, enabling > 500x coverage for 95% of amplicons at > 5,000x mean coverage.

Sequence data generated from TruSight Myeloid libraries are analyzed using the on-instrument MiSeq Reporter software. After demultiplexing and FASTQ file generation, the software uses a custom banded Smith-Waterman aligner to align the reads against the human hg10 reference genome to create BAM files. The Somatic Variant Caller then performs variant analysis for the specified regions. The outputs are VCF or gVCR files, which are text files that contain SNPs and small indels.

Limitations

This test may not detect all variants in non-coding regions that could affect gene expression or copy number changes encompassing all or a large portion of the gene.

DRAFT REPORT