Chromosomal alterations of pediatric malignancy in a West Texas population

Aditya Rajan; Sahil Tonk; Chhanda Bose; Sharda Singh; Sriman Swarup; Santosh Chavali; Kishore Bhende; Philip Palade; Ashly Hindle; Meenakshi Darden; Vijay Tonk; Sanjay Awasthi

doi:10.12746/swrccc.v8i33.627

Chromosomal alterations of pediatric malignancy in a West Texas population

Aditya Rajan
, Sahil Tonk
, Chhanda Bose
, Sharda Singh
, Sriman Swarup
, Santosh Chavali
, Kishore Bhende
, Philip Palade
, Ashly Hindle
, Meenakshi Darden
, Vijay Tonk
, Sanjay Awasthi

Research output: Contribution to journal › Article

Abstract

Background: Comparative genomic hybridization (CGH) microarrays are used forgenome-wide evaluation of copy number variations (CNV) of known prognostic significance;however, unannotated variants of uncertain significance (VUS) are frequently present. Toidentify potentially actionable targets, we retrospectively analyzed VUS loci using CGH datafrom 192 cases of cancer or genetic disorders treated at TTUHSC.Methods: DNA was hybridized onto CytoSure Constitution V3 arrays, scanned with theAgilent microarray D scanner, and analyzed by CytoSure Interpret Software.Results: We found 794 distinct CNVs, the most frequent being 14q32.22 (112rearrangements), 14q11.2 (100), 8p11.2 (98), 15q11.1-q11.2 (83), and 8p23.1 (77). In particular,8p11.22 alterations were found in many pediatric tumors, with gain/loss ratio of 4.7. Linkage ofTACC1, TM2D2, KAT6A and ADAM32 was indicated by a similar 5-year survival rate of 75.3%(n = 253), which was greater than in unaltered cases (62.2%, n = 15,809 cases) in The CancerGenome Atlas database.Conclusion: Knockdown of genes occurring at variants of uncertain significance (VUS)loci may help identify new therapy targets.

Original language	American English
Pages (from-to)	7-20
Number of pages	14
Journal	The Southwest Respiratory and Critical Care Chronicles
Volume	8
Issue number	33
DOIs	https://doi.org/10.12746/swrccc.v8i33.627
State	Published - Sep 2020

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@article{7956a66c4e0f4e4eb481fe50198a94e4,

title = "Chromosomal alterations of pediatric malignancy in a West Texas population",

abstract = "Background: Comparative genomic hybridization (CGH) microarrays are used forgenome-wide evaluation of copy number variations (CNV) of known prognostic significance;however, unannotated variants of uncertain significance (VUS) are frequently present. Toidentify potentially actionable targets, we retrospectively analyzed VUS loci using CGH datafrom 192 cases of cancer or genetic disorders treated at TTUHSC.Methods: DNA was hybridized onto CytoSure Constitution V3 arrays, scanned with theAgilent microarray D scanner, and analyzed by CytoSure Interpret Software.Results: We found 794 distinct CNVs, the most frequent being 14q32.22 (112rearrangements), 14q11.2 (100), 8p11.2 (98), 15q11.1-q11.2 (83), and 8p23.1 (77). In particular,8p11.22 alterations were found in many pediatric tumors, with gain/loss ratio of 4.7. Linkage ofTACC1, TM2D2, KAT6A and ADAM32 was indicated by a similar 5-year survival rate of 75.3\%(n = 253), which was greater than in unaltered cases (62.2\%, n = 15,809 cases) in The CancerGenome Atlas database.Conclusion: Knockdown of genes occurring at variants of uncertain significance (VUS)loci may help identify new therapy targets.",

author = "Aditya Rajan and Sahil Tonk and Chhanda Bose and Sharda Singh and Sriman Swarup and Santosh Chavali and Kishore Bhende and Philip Palade and Ashly Hindle and Meenakshi Darden and Vijay Tonk and Sanjay Awasthi",

year = "2020",

month = sep,

doi = "10.12746/swrccc.v8i33.627",

language = "American English",

volume = "8",

pages = "7--20",

journal = "The Southwest Respiratory and Critical Care Chronicles",

number = "33",

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TY - JOUR

T1 - Chromosomal alterations of pediatric malignancy in a West Texas population

AU - Rajan, Aditya

AU - Tonk, Sahil

AU - Bose, Chhanda

AU - Singh, Sharda

AU - Swarup, Sriman

AU - Chavali, Santosh

AU - Bhende, Kishore

AU - Palade, Philip

AU - Hindle, Ashly

AU - Darden, Meenakshi

AU - Tonk, Vijay

AU - Awasthi, Sanjay

PY - 2020/9

Y1 - 2020/9

N2 - Background: Comparative genomic hybridization (CGH) microarrays are used forgenome-wide evaluation of copy number variations (CNV) of known prognostic significance;however, unannotated variants of uncertain significance (VUS) are frequently present. Toidentify potentially actionable targets, we retrospectively analyzed VUS loci using CGH datafrom 192 cases of cancer or genetic disorders treated at TTUHSC.Methods: DNA was hybridized onto CytoSure Constitution V3 arrays, scanned with theAgilent microarray D scanner, and analyzed by CytoSure Interpret Software.Results: We found 794 distinct CNVs, the most frequent being 14q32.22 (112rearrangements), 14q11.2 (100), 8p11.2 (98), 15q11.1-q11.2 (83), and 8p23.1 (77). In particular,8p11.22 alterations were found in many pediatric tumors, with gain/loss ratio of 4.7. Linkage ofTACC1, TM2D2, KAT6A and ADAM32 was indicated by a similar 5-year survival rate of 75.3%(n = 253), which was greater than in unaltered cases (62.2%, n = 15,809 cases) in The CancerGenome Atlas database.Conclusion: Knockdown of genes occurring at variants of uncertain significance (VUS)loci may help identify new therapy targets.

AB - Background: Comparative genomic hybridization (CGH) microarrays are used forgenome-wide evaluation of copy number variations (CNV) of known prognostic significance;however, unannotated variants of uncertain significance (VUS) are frequently present. Toidentify potentially actionable targets, we retrospectively analyzed VUS loci using CGH datafrom 192 cases of cancer or genetic disorders treated at TTUHSC.Methods: DNA was hybridized onto CytoSure Constitution V3 arrays, scanned with theAgilent microarray D scanner, and analyzed by CytoSure Interpret Software.Results: We found 794 distinct CNVs, the most frequent being 14q32.22 (112rearrangements), 14q11.2 (100), 8p11.2 (98), 15q11.1-q11.2 (83), and 8p23.1 (77). In particular,8p11.22 alterations were found in many pediatric tumors, with gain/loss ratio of 4.7. Linkage ofTACC1, TM2D2, KAT6A and ADAM32 was indicated by a similar 5-year survival rate of 75.3%(n = 253), which was greater than in unaltered cases (62.2%, n = 15,809 cases) in The CancerGenome Atlas database.Conclusion: Knockdown of genes occurring at variants of uncertain significance (VUS)loci may help identify new therapy targets.

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U2 - 10.12746/swrccc.v8i33.627

DO - 10.12746/swrccc.v8i33.627

M3 - Article

VL - 8

SP - 7

EP - 20

JO - The Southwest Respiratory and Critical Care Chronicles

JF - The Southwest Respiratory and Critical Care Chronicles

IS - 33

ER -

Chromosomal alterations of pediatric malignancy in a West Texas population

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