Questions on Biopsy Results

My sister just got her results back from a recent biopsy. I wanted to get your guys input on it as it looks different from the original results we got from her resection and her genetic testing (which I knew would not b as in depth). I m wondering if this is sufficient to confirm its low grade glio cells? As doesn't have methylation or all the other stuff To determine grade (ki) auto correct sorry! Do u guys think I should aske her to ask for the biopsy report or this is sufficient? I would want as much info as possible but need others input before I mention to her as this may b enuf and I m missing it? Those results were from diff brain tumor centers then this one. Quick background: she's 34, dx Dec 14, secondary GBM, IDH1, partially methylated, P53, she had a Cple others that came up but I have to get her report from 14' and dble check. We were told they were ones nothing was being done w though and these were the major ones.  After rad/chemo an area of enhancement showed on MRI. She chose to stick w tmz. She's stayed on the 5/23 for over 16 months and the area has stayed stable. They did 2 PETs that showed no active cancer cells but we're still concerned so last month did biopsy to b sure. At first told her no more chemo as preliminary testing said it was necrosis. Well, then got call saying it had some low grade cancer glio cancer cells. At first dr Friedman recommended 6 more mths of 5/23 but cause my sis really does not want to do it they talked and he agreed to the metronomic sched. (80 mg tmz daily) but w my reading and the IDH1 I wanted your opinion on it or if something should b added? Read study from Perry. If I can upload her genetic testing what am I looking for, w regards to the idh1 that u were talking about earlier w Logan? She handled tmz 5/23 really fine (mostly gi issues, lost some weight, her absolute lymphocytes cont to drop but everything else ok and not low enuf to have to wait or anything for a cycle). She's only doing THC/CBD as Duke was against all supplements, other meds she was on. And they go by what they r mostly told, to a point. I still research, get info, trials ready (in case none at Duke work out and they don't go for avastin, if that's recommended). It's left parietal lobe.

Thanks u so much for any help w this and as always u guys and your luved ones r all in my thoughts daily.

Kylie

Unstained slides, SP16-22791 A1 (IDH1 Targeted Mutation Analysis with Reflex to IDH2 Mutation Analysis):

Positive.

IDH1 mutation detected. p.Arg132His (c.395G>A).
See comment and objective findings.

Comment: A single mutation was detected. The p.Arg132His IDH1 alteration is a previously cited mutation seen in CNS neoplasms (see references).

Isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) are NADP+ dependent enzymes that catalyze the conversion of isocitrate to alpha-ketoglutarate and are key components in the mitochondrial citric acid cycle. Acquired point mutations in primary CNS neoplasms have been described in codon 132 of IDH1 (predominantly Arg132His, but also Arg132Cys, Arg132Ser, Arg132Leu and Arg132Gly) and the analogous amino acid in IDH2 (Arg172Gly, Arg172Lys and Arg172Met). A high percentage of WHO grade II and grade III astrocytic and oligodendroglial neoplasms contain IDH1 or IDH2 mutations, including diffuse astrocytomas (II), oligodendrogliomas (II), anaplastic astrocytomas and oligodendrogliomas (III) and anaplastic oligoastrocytomas (III). IDH1 and IDH2 mutations are also common in secondary glioblastomas (IV) but are rarely found in primary adult or pediatric glioblastomas (IV). In patients with glioblastomas or anaplastic astrocytomas, the presence of an acquired IDH1 or IDH2 mutation is associated with longer overall survival. Multiple factors contribute to prognosis in patients with primary CNS neoplasms. Thus, this assay is intended for use as an aid in developing patient-specific prognostic predictions but is not a substitute for a complete pathologic and clinical evaluation, or physician's judgment and clinical experience.

The sensitivity and specificity of DNA sequencing is high for the detection of nucleotide base changes, small deletions, and insertions in the regions analyzed. This assay may not detect an acquired mutation that is present below the 15% detection limit (i.e., mutant cell population of <30%). Only amino acids 69-138 of the IDH1 gene and amino acids 126-178 of the IDH2 gene were examined. Changes outside of this region will not be detected. The presence of a mutant population containing a large deletion, duplication, insertion, aberrant splicing, or sequence alteration adversely affecting primer binding may not be identified using these methods. Mutations or polymorphisms in the DNA oligonucleotide primer binding regions, poor DNA quality, insufficient DNA quantity or the presence of PCR inhibitors can result in uninterpretable or (rarely) inaccurate results. For additional information or for help interpreting the results of this test, clinicians should contact the DUHS Clinical Molecular Diagnostics Laboratory. Patients should contact their healthcare provider with any questions related to this report.

References:

Balss J, et al. Analysis of the IDH1 codon 132 mutation in brain tumors. Acta Neuropathol. 2008;116:597-602.

Yan H, et al. IDH1 and IDH2 mutations in gliomas. N Engl J Med. 2009;360(8):765-73.

Laboratory Director:
                   Siby Sebastian, Ph.D., ABMG; DABCC
                   Associate Director, Molecular Diagnostics
   Clinical History
   
Persistent glioma, low grade
   Sample Type
   
Unstained slides, SP16-22791 A1
   Test Performed
   
IDH1 Targeted Mutation Analysis with Reflex to IDH2 Mutation Analysis
   Objective Findings
   
Complete coverage of IDH1 exon 4 (amino acids 69-138) was obtained using forward and reverse sequencing primers. These sequences were compared to the reference DNA sequence (GenBank Accession: NM_005896.2).

The following sequence change was detected: 
Gene
Location
Type
c.
p.
Normal sequence
IDH1
exon 4
missense
c.395G>A
p.Arg132His
Detected


   Methodology
   
This assay uses PCR amplification followed by Sanger DNA sequencing to detect point mutations in exon 4 of the IDH1 gene, with reflex testing to detect point mutations in exon 4 of the IDH2 gene for all IDH1 negative cases. An H&E stained slide for each case is first evaluated to identify the regions of greatest tumor content. These regions are then macro-dissected from adjacent unstained formalin-fixed paraffin-embedded sections and used to prepare genomic DNA. The protein coding and flanking intronic sequences of IDH1 exon 4 (containing codon 132), and, if reflex testing is performed, IDH2 exon 4 (containing codon 172) are amplified from this purified genomic DNA by PCR. The primers used in these PCR reactions contain M13 universal primer "tails" at their 5' ends, and have 3' ends that are complementary to their genomic target sequence. The resulting PCR products are treated with an exonuclease/phosphatase mixture (ExoSAP-IT) to remove excess PCR primers and nucleotides. These purified DNA amplicons are then sequenced using universal M13 forward and reverse sequencing primers (M13 Forward/-20 and M13 Reverse/-27) and the Big Dye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems). The products of the completed sequencing reactions are purified with the Big Dye XTerminator Purification Kit and resolved using the ABI Genetic Analyzer. Data is analyzed using the ABI Data Collection software, Sequencing Analysis software, and SeqScape software. Sequences are compared to the reference DNA sequence for the IDH1 and IDH2 genes (GenBank Accession IDH1: NM_005896.2; IDH2: NM_002168.2).
   Disclaimer
   
This test was developed and its performance characteristics determined by the DUHS Clinical Molecular Diagnostics Laboratory. It has not been cleared or approved by the U.S. Food and Drug Administration. This test is used for clinical purposes. It should not be regarded as investigational or for research. This laboratory is certified under the Clinical Laboratory Improvement Amendments of 1988 ("CLIA") as qualified to perform high complexity clinical testing.

Results
   Document on 7/31/2016  9:09 PM by Castellar Edgar R

Lab and Collection
   IDH1 Targeted Mutation Analysis with Reflex to IDH2 Mutation Analysis on 7/21/2016