| Literature DB >> 25188507 |
Benedict Yan1, Chik Hong Kuick1, Malcolm Lim1, Kavita Venkataraman2, Chandana Tennakoon3, Eva Loh1, Derrick Lian1, May Ying Leong1, Manikandan Lakshmanan4, Vinay Tergaonkar4, Wing-Kin Sung5, Shui Yen Soh6, Kenneth T E Chang1.
Abstract
ALK is an established causative oncogenic driver in neuroblastoma, and is likely to emerge as a routine biomarker in neuroblastoma diagnostics. At present, the optimal strategy for clinical diagnostic evaluation of ALK protein, genomic and hotspot mutation status is not well-studied. We evaluated ALK immunohistochemical (IHC) protein expression using three different antibodies (ALK1, 5A4 and D5F3 clones), ALK genomic status using single-color chromogenic in situ hybridization (CISH), and ALK hotspot mutation status using conventional Sanger sequencing and a next-generation sequencing platform (Ion Torrent Personal Genome Machine (IT-PGM)), in archival formalin-fixed, paraffin-embedded neuroblastoma samples. We found a significant difference in IHC results using the three different antibodies, with the highest percentage of positive cases seen on D5F3 immunohistochemistry. Correlation with ALK genomic and hotspot mutational status revealed that the majority of D5F3 ALK-positive cases did not possess either ALK genomic amplification or hotspot mutations. Comparison of sequencing platforms showed a perfect correlation between conventional Sanger and IT-PGM sequencing. Our findings suggest that D5F3 immunohistochemistry, single-color CISH and IT-PGM sequencing are suitable assays for evaluation of ALK status in future neuroblastoma clinical trials.Entities:
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Year: 2014 PMID: 25188507 PMCID: PMC4154751 DOI: 10.1371/journal.pone.0106575
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Commercially available monoclonal ALK antibodies.
| Clone | Tumor type studied | Company | Reference |
| ALK1 | Neuroblastoma | DAKO Denmark A/S, Glostrup, Denmark | De Brouwer 2010 |
| D5F3 | Lung adenocarcinoma | Cell Signaling, Danvers, MA, USA | Ying 2013 |
| RM-9108 | Neuroblastoma | Thermo Fisher Scientific, Fremont, CA, USA | Duijkers 2012 |
| 5A4 | Neuroblastoma | Thermo Fisher Scientific, Fremont, CA, USA | Passoni 2009 |
Clinicopathological characteristics of study cohort.
| Age at first biopsy (yrs, N = 95) | |
| Mean (Range) | 3.54 (0.02–10.94) |
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| Male | 60 |
| Female | 35 |
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| Pre-treatment primary tumors | 36 |
| Post-treatment primary tumors | 53 |
| Relapsed/metastatic tumors | 26 |
| Treatment status unknown | 3 |
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| Neuroblastoma | 67 |
| Ganglioneuroblastoma | 16 |
| Ganglioneuroma | 3 |
| Neuroblastic tumor, unspecified | 32 |
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| Amplified | 26 |
| Non-amplified | 81 |
| Equivocal | 1 |
Antibodies used in this study with corresponding platforms.
| Clone (dilution) | Company | Platforms | Antigen Retrieval |
| ALK1 (1∶25) | DAKO Denmark A/S, Glostrup, Denmark | Ventana Benchmark ULTRA (Ventana Medical Systems, AZ, USA) | CC1 solution (Ventana Medical Systems, AZ, USA) for 36 min |
| D5F3 (1∶100) | Cell Signaling, Danvers, MA, USA | Ventana Benchmark XT (Ventana Medical Systems, AZ, USA) | CC1 solution (Ventana Medical Systems, AZ, USA) for 64 min |
| 5A4 (1∶60) | Leica Biosystems, Newcastle Upon Tyne, UK | Ventana Benchmark XT (Ventana Medical Systems, AZ, USA) | CC1 solution (Ventana Medical Systems, AZ, USA) for 64 min |
Sample type and ALK immunohistochemical expression (N = 105).
| ALK1 clone | 5A4 clone | D5F3 clone | |||||||||
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| 0 | 1+ | 3+ | 0 | 1+ | 2+ | 3+ | 0 | 1+ | 2+ | 3+ |
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| 28 | 0 | 0 | 20 | 5 | 3 | 0 | 11 | 8 | 6 | 3 |
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| 49 | 0 | 1 | 41 | 7 | 1 | 1 | 17 | 19 | 9 | 5 |
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| 23 | 1 | 0 | 15 | 5 | 3 | 1 | 4 | 10 | 4 | 6 |
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| 3 | 0 | 0 | 1 | 2 | 0 | 0 | 1 | 0 | 2 | 0 |
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| 0.519 | 0.165 | 0.322 | ||||||||
Figure 1ALK CISH and IHC of an ALK amplified case.
(A) CISH (B) ALK1 IHC (C) 5A4 IHC (D) D5F3 IHC.
Figure 2ALK CISH and IHC of an ALK non-amplified case.
(A) CISH (B) ALK1 IHC (C) 5A4 IHC (D) D5F3 IHC.
Correlation between ALK1 IHC and ALK CISH (N = 91).
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| 1 | 0 |
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| 0 | 90 |
p (Fisher's exact test) = 0.011.
Correlation between 5A4 IHC and ALK CISH (N = 91).
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| 1 | 1 |
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| 0 | 89 |
p (Fisher's exact test) = 0.022.
Correlation between D5F3 IHC and ALK CISH (N = 91).
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| 1 | 12 |
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| 0 | 78 |
p (Fisher's exact test) = 0.143.
ALK mutations detected by both Sanger sequencing and IT-PGM.
| Case Number | Coding DNA | Amino acid | Depth of Coverage (x) | Variant allele frequency (%) |
| 11011 | c.3522C>G | p.F1174L | 1992 | 50.45 |
| 145808 | c.3522C>A | p.F1174L | 782 | 15.09 |
| 70309 | c.3824G>A | p.R1275Q | 897 | 20.07 |
| 180713 | c.3824G>A | p.R1275Q | 1536 | 41.99 |
| 184213 | c.3522C>A | p.F1174L | 1996 | 56.21 |
Correlation between ALK D5F3 IHC score and mutation status.
| p.F1174L | p.R1275Q | p.F1174 and p.R1275 wild-type | |
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| 1 | 2 | 5 |
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| 2 | 0 | 11 |
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| 0 | 0 | 21 |
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| 0 | 0 | 12 |
p (Fisher's exact test) = 0.004.
Figure 3Depth of coverage of amplicons from 5′ to 3′.
The p.F1174 and p.R1275 hotspots are covered by the amplicons marked with a red and purple arrow respectively.
Figure 4Depth of coverage and GC content.
(A) The red dashed line indicates the GC content. The X-axis shows the amplicons ordered with increasing depth of coverage from left to right. (B) There is a negative correlation between depth of coverage and GC content; this is not statistically significant (R2 = 0.1).
Figure 5IGV (IT-PGM) and Sanger sequences of ALK hotspot mutations.
(A) c.3522C>G (p.F1174L) mutation. (B) c.3824G>A (p.R1275Q) mutation.