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Just wanted to share about CanVigs' gene specific guidelines which we use for variant interpretation of BRCA1/2 and other genes. Very useful, including gene specific important domains/residues and sources of evidence to aid classification.

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Use of FISH CDKN2A Deletion Testing for Detection of Mesothelioma

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Use of FISH CDKN2A Deletion Testing for Detection of Mesothelioma

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Hi Just wondering if we will be expected to refer to or know the findings of the pilot studied described in this lecture. I am unsure how this relates to our learning outcomes, other than the considerations of FISH testing in mesothelioma? Thanks!

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For the student that emailed about the decision making...

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Do you foresee that ctDNA testing will be introduced into all genomic laboratories for rapid testing, such as Case 3 in "Genomic Methods Employed in Molecular Lung Cancer Testing"? I realise it is in its early stages, but currently, only a few provide this, which requires sending ctDNA out of regions and further introducing delays to reporting, which is counter intuitive of rapid testing and equality of the NHS.

Just wondered on your thoughts. Thanks

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Could you please clarify the correlation between the TPS score and PDL-1 expression. Dr. Quinn mentions that someone with a PDL-1 expression of >50% is eligible for 1st line therapy and one with a TPS score of >1% is eligible for 2nd line therapy. Thanks.

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Hi can I just confirm that the Cutting Edge research to inform new treatment strategies was optional content? Thanks

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Ovarian Cancer cutting Edge Research to inform New Treatment strategies

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Ovarian Cancer cutting Edge Research to inform New Treatment strategies

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Hi just wondering is this whole section optional as it seems it may be from the timetable but doesn't indicate it in the section? whilst it would be good to review in the interest of time if its optional and therefore not assessed I will review after the assessment to support my training and development. As its going to be tight to get it all done before Friday

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There has been quite a few detailed slides and lectures which focus on histopathology. What level of detail are we expected to know, with regards to histopathology?

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A couple of the questions weren't covered in the online lectures, is this material that will be covered in the live session? or is there material missing that we need to review to prepare for the assessment on Friday?

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Characterising the loss-of-function impact of 5′ untranslated region variants in 15,708 individuals - PubMed

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Upstream open reading frames (uORFs) are tissue-specific cis-regulators of protein translation. Isolated reports have shown that variants that create or disrupt uORFs can cause disease. Here, in a systematic genome-wide study using 15,708 whole genome sequences, we show that variants that create new …

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Rates of Ovarian and Breast Cancer for BRCA1/2 Variant Carriers

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Rates of Ovarian and Breast Cancer for BRCA1/2 Variant Carriers

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There is an issue with the breast/ovarian cancer risk statistics quoted for BRCA1/2 variant carriers where different lecturers have quoted quite different statistics. In "Genomic Testing for Ovarian Cancer" the lifetime ovarian cancer rates are given as 69 and 17% for BRCA1/2 variant carriers respectively - drawn from the Mavaddat et al. 2013 paper. In the "Impact of Genetic Testing on Breast Cancer Treatment Decisions", however, these are given as 44 and 17% respectively- drawn from the Kuchenbaecker et al. 2017 paper. The breast cancer statistics are similarly discordant. Given that this was one of the practice MCQs for ovarian cancer, how are we supposed to determine which value is sought as the "correct" answer to an MCQ?

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Hi! For NGS data for somatic ovarian cancer testing linking with the 2 hit hypothesis,would you be expected to pick up two loss of function variants for say BRAC1? Or is one variant just picked up?

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I don't think the slides in case study 2 were from that patient! :D

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It is usual to do FISH on blood for metastatic lung patients? Are there high enough numbers of circulating tumour cells? Can you select for them within the sample?

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Hi I was just wondering why the practice question "which of the following represents newly identified genomic target relevant to targeted therapies in breast cancer" had the correct answer ALK/ROS1 fusions and not ESR1 ligand binding domain variants? is it as ESR1 testing is recommended but not on the test directory yet? Just wondering as this question didnt specify to be in accordance to the test directory. Or does ESR1 not count as a newly identified genomic target relevant to targeted therapies in breast cancer? Thanks

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I enjoyed these lectures however, the molecular information was sparce. The focus seems to be on morphological tumour categorisation. Will the exam questions reflect this? Do we need to know epidemiological information for example?

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I'm wondering about the UMI's. In these slides (genetic testing for ovarian cancer part 3) it is shown that there is a high mean sample UMI but then only one variant has a UMI. The UMI is absent in the discounted calls. How can it be absent? Aren't all the molecules tagged with the UMI?