High allele frequency of somatic mutationJun Kang2019 11 11 / 26

Question 1

Can we determine whether the variant is germline or somatic using allele frequency and tumor percentage in tumor only test?

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BRCA resultBRCA1 mutation: Positive - p.Glu649Ter (c.1945G>T)  
Variant allele frequency 63.84%  
Tumor cell percentage: 70%  
BRCA negative in blood sample
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Question 2

Is it possible 64% allele frequency of somatic mutation?

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Variant allele frequency in clinical tumor sample

$A l l e l e f r e q u e n c y \approx R e a d c o u n t$

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Somatic variant, Two copy, Tumor cellularity 50%

Variant allele frequency?

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Germline variant, Heterozigosity, Two copy, Tumor cellularity 25%

Variant allele frequency?

class: center

Germline variant, Heterozigosity, Two copy, Tumor cellularity 50%

Variant allele frequency?

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Hypothesis

Germline, homo
Germline, hetero
Somatic


 100%
50%
half of tumor cellularity, ≤50%≤50%

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Germline, homo	Germline, hetero	Somatic
100%	50%	half of tumor cellularity, $\leq 50 %$

Germline variant, Heterozigosity, One copy, LOH, Tumor cellularity 50%

Variant allele frequency?

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Germline variant, Heterozigosity, One copy, LOH, Tumor cellularity 25%

Variant allele frequency?

10 / 26

Somatic variant, One copy, LOH, Tumor cellularity 50%

Variant allele frequency?

11 / 26

Somatic variant, Amplification, Tumor cellularity 25%

Variant allele frequency?

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Variant allele frequency in clinical tumor sampleGermline vs somatic  
Tumor cell proportion  
Loss of heterozygosity 
Copy number  
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Allele frequency in Somatic vs Germline in tumor only sampleBRCA1 mutation: Positive - p.Glu649Ter (c.1945G>T)  
Variant allele frequency 63.84%  
Tumor cell percentage: 70%  
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Allele frequency[1]

$A F_{g e r m l i n e}$ $=$ $\frac{p V + 1 - p}{p C + 2 (1 - p)}$
$A F_{s o m a t i c}$ $=$ $\frac{p V}{p C + 2 (1 - p)}$

Given copy number (C)
Variant allele count (V)
Sample purity (p)
Variant status (somatic or germline)

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Limited information

What we know
What we don't know


Tumor cell percentage
Copy number

Variant allele frequency
LOH

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What we know	What we don't know
Tumor cell percentage	Copy number
Variant allele frequency	LOH

Error

Tumor cell percentage
Allele frequency

$A l l e l e f r e q u e n c y ≉ R e a d c o u n t$

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BRCA mutation and LOH [2]

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Allele frequencyBRCA1 mutation: Positive - p.Glu649Ter (c.1945G>T)  
Variant allele frequency 63.84%  
Tumor cell percentage: 70% -> 80%  
Somatic (supposed)  
LOH (supposed)  
One copy (supposed)  
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Allele frequency

$A F_{s o m a t i c}$ $=$ $\frac{p V}{p C + 2 (1 - p)}$ $= 0.67$

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Allele frequencyBRCA1 mutation: Positive - p.Glu649Ter (c.1945G>T)  
Variant allele frequency 63.84%  
Tumor cell percentage: 70% -> 60%  
Germline (supposed)  
LOH (supposed)  
One copy (supposed)  
21 / 26

Allele frequency

$A F_{g e r m l i n e}$ $=$ $\frac{p V + 1 - p}{p C + 2 (1 - p)}$ $= 0.71$

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Someone ask ...

Does tumor only NGS test distinguish a variant somatic and germline?
Answer 'No'

Is it possible 64% allele frequency of somatic BRCA variant?
Answer 'Yes, It is when BRCA somatic variant accompanied with LOH'

23 / 26

Germline variant, One copy, LOH, Tumor cellularity 100% (Bonus1)

Allele frequency 100% hetero germline variant

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Somatic variant, Amplification, Hetero, Tumor cellularity 100% (Bonus2)

Allele frequency 90% somatic variant

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References

[1] J. X. Sun, Y. He, E. Sanford, et al. "A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal". En. In: PLOS Computational Biology 14.2 (2018), p. e1005965. ISSN: 1553-7358.

[2] M. M. de Jonge, D. Ruano, R. van Eijk, et al. "Validation and Implementation of BRCA1/2 Variant Screening in Ovarian Tumor Tissue". In: The Journal of Molecular Diagnostics 20.5 (9. 2018), pp. 600-611. ISSN: 1525-1578.

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High allele frequency of somatic mutation

Jun Kang

2019 11 1

Question 1

BRCA result

Question 2

Variant allele frequency in clinical tumor sample

Somatic variant, Two copy, Tumor cellularity 50%

Germline variant, Heterozigosity, Two copy, Tumor cellularity 25%

Germline variant, Heterozigosity, Two copy, Tumor cellularity 50%

Hypothesis

Germline variant, Heterozigosity, One copy, LOH, Tumor cellularity 50%

Germline variant, Heterozigosity, One copy, LOH, Tumor cellularity 25%

Somatic variant, One copy, LOH, Tumor cellularity 50%

Somatic variant, Amplification, Tumor cellularity 25%

Variant allele frequency in clinical tumor sample

Allele frequency in Somatic vs Germline in tumor only sample

Allele frequency[1]

Limited information

Error

BRCA mutation and LOH [2]

Allele frequency

Allele frequency

Allele frequency

Allele frequency

Someone ask ...

Germline variant, One copy, LOH, Tumor cellularity 100% (Bonus1)

Somatic variant, Amplification, Hetero, Tumor cellularity 100% (Bonus2)

References

Question 1

Help