NCIH2171_LUNG


Available Data

  • Vendor Karyotype
  • ecDNA Presence Verification from Literature
  • Amplicon Architect Prediction
  • Circle Hunter Prediction
  • Shatterseek Prediction

ID Value
ATCC CRL-5929
DSMZ ACC-544
Cellosaurus NCI-H2171
Cosmic 688015.0

Property Value
% Polyploidy 8.0
Ploidy Classification hypodiploid
Modal Chromosome Number None
Modal Range Numeric 42-44
Marker Chromosomes Average Field 4.0
Primary or Metastasis Metastasis
Count of SV's 10

Details

ecDNA Present (Y/N/P): Y

Literature source: https://genome.cshlp.org/content/17/9/1296.short
https://www.sciencedirect.com/science/article/pii/S0165460805001561#bib10
https://aacrjournals.org/cancerdiscovery/article/13/4/928/725029/Extrachromosomal-DNA-Amplification-Contributes-to

HSR Classification: N

ATCC Karyotype: iso(3q)

DSMZ Karyotype: human hypodiploid karyotype with 8% polyploidy - 42-44<2n>XY, -4, -5, -8, -10, -11, -13, -15, -17, -19, +20, +4-5mar, add(1)(p36), der(2)ins(2;?)(p2?;?)t(2;2)(q37;p24), add(3)(p11), i(3q), del(6)(q25q26), del(9)(p11), der(12)add(12)(p11)del(12)(q24), add(14)(p11), i(15q), add(18)(p11)

Heterogeneity Indications and Other Notes: No data

Download Breakpoint Edges CSV

Prediction

ecDNA Amplicon Predicted: Y

Predicted Amplicon Classes: ['ecDNA', 'Linear amplification', 'BFB']

Predicted Genes on ecDNA

['ACRBP', 'ACSM4', 'ANO2', 'APOBEC1', 'ARNTL2', 'ARNTL2-AS1', 'ASPH', 'ATN1', 'C12orf57', 'C1R', 'C1RL', 'C1RL-AS1', 'C1S', 'C3AR1', 'CASC11', 'CASC19', 'CASC21', 'CASC8', 'CCAT1', 'CCAT2', 'CCDC81', 'CCDC83', 'CCDC89', 'CCDC91', 'CCND2', 'CCND2-AS1', 'CD163', 'CD163L1', 'CD27', 'CD27-AS1', 'CD4', 'CD9', 'CDCA3', 'CHD4', 'CHD7', 'CLEC4A', 'CLEC4C', 'CLEC4D', 'CLEC6A', 'CLSTN3', 'CLVS1', 'COPS7A', 'CRACR2A', 'CREBZF', 'DPPA3', 'DSTNP2', 'EED', 'EMG1', 'ENO2', 'ERGIC2', 'FAM66C', 'FAM86FP', 'FAM90A1', 'FAR2', 'FOXJ2', 'GAPDH', 'GDF3', 'GGH', 'GNB3', 'GOLT1B', 'GPR162', 'GYS2', 'HIKESHI', 'IAPP', 'IFFO1', 'ING4', 'KLHL42', 'LAG3', 'LDHB', 'LPAR5', 'LPCAT3', 'LRRC23', 'LTBR', 'MANSC4', 'ME3', 'MLF2', 'MRPL51', 'MRPS35', 'MYC', 'NANOG', 'NANOGNB', 'NCAPD2', 'NECAP1', 'NKAIN3', 'NKAIN3-IT1', 'NOP2', 'OXA1L', 'P3H3', 'PARP11', 'PCAT1', 'PCAT2', 'PEX5', 'PHB2', 'PIANP', 'PICALM', 'PLEKHG6', 'POU5F1B', 'POU5F1P3', 'PPFIBP1', 'PRMT8', 'PRNCR1', 'PTHLH', 'PTMS', 'PTPN6', 'PVT1', 'PYROXD1', 'RBP5', 'RECQL', 'REP15', 'RNU7-1', 'RPL13P5', 'SCARNA10', 'SCARNA11', 'SCARNA12', 'SCNN1A', 'SLC2A14', 'SLC2A3', 'SLC7A7', 'SLCO1A2', 'SLCO1B1', 'SLCO1B3-SLCO1B7', 'SLCO1B7', 'SMCO2', 'SNORA120', 'SPSB2', 'SPX', 'STK38L', 'SYTL2', 'TAPBPL', 'THCAT155', 'TIGAR', 'TMEM126A', 'TMEM126B', 'TNFRSF1A', 'TPI1', 'TTPA', 'USP5', 'VAMP1', 'VWF', 'YTHDF3', 'YTHDF3-AS1', 'ZNF384', 'ZNF705A']

Predicted Features

Class Amplicon Complexity Score
ecDNA 1 2.122404296
Image 1

Class Amplicon Complexity Score
Linear amplification 2 0.0
Image 2

Class Amplicon Complexity Score
BFB 3 1.284327416
Image 3

Prediction

ecDNA: negative


Prediction

Shatterseek Prediction: High Confidence

Shatterseek High Confidence Chromosomes: 8

Shatterseek Low Confidence Chromosomes: 5