A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data

A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data

Motivation: The tumor is composed of different cancer cell population (clones), which continues to adapt to their local microenvironment. the standard method for deconvolution clonal mutation group seeks to identify and estimate the prevalence of each group in the tumor, while taking into account the purity and copy number profile. This method has been applied to a cross-sectional and longitudinal data after removing information about the time of sample collection.

Two key question is how we can combine the information in our analyzes and there are benefits in doing so?
Results: We developed clonal deconvolution method, which combines explicit temporal distance longitudinal tumor samples. By combining the Dirichlet Process Mixture Model Gaussian Process priors and used as an input sequence is rarely collected several samples, our method can reconstruct the temporal profile mutation abundance of each cluster is supported by data as a continuous function of time.

We refer to our method on the whole genome, whole exome and sequencing data targeted from patients with chronic lymphocytic leukemia, the data biopsy fluid of patients with melanoma and synthetic data and we found that combining information about a collection of networks improve the performance of the model, as long as the data volume and complexity is available for the free estimate model parameters. Thus, our approach is very useful when collecting a relatively long sequences of tumor samples feasible, such as in liquid cancers (eg, leukemia) and liquid biopsy.


Bactrian camel population size smaller than the dromedary, and they are distributed in the cold and mountain regions and also at risk of extinction in some countries such as Iran. To identify and investigate genome-wide variation, whole-genome sequencing of two Bactrian camels Iran do with the scope 37.4- and 42.6-fold for the first time. Along with Iran Bactrian camel, sequencing data from two domestic and two Mongolian wild Bactrian camel is stored in the NCBI reanalyzed.

 A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data
A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data

scPADGRN: An asphalt ADMM approach to reconstruct gene regulatory networks dynamically using RNA sequencing data-single cell

development and cell differentiation disease both involve dynamic changes; Therefore, reconstruction of dynamic gene regulatory network (DGRNs) is an important issue but it is difficult in biological systems. With recent advances in single-cell technical RNA sequencing (scRNA-seq), a large volume of data scRNA-seq is being obtained for the various processes. However, current methods of concluding DGRNs of the bulk sample may not be suitable for data-seq scRNA.

In this work, we present scPADGRN, inference DGRN new method using “time-series” scRNA-seq data. scPADGRN combining the method of alternating directions asphalt multiplier by grouping cells for reconstruction DGRN. It shows the advantages in accuracy, robustness and fast convergence. In addition, so-called quantitative index Differentiation Gene Interactions Enrichment (DGIE) served to measure the interaction enrichment of genes related to differentiation.

From the score DGIE of the relevant subnetwork, we conclude that the function of embryonic stem (ES) cells are most active initially and may gradually fade over time. Communication power of genes contribute to note that facilitate the differentiation of cells increased from ES cells differentiated into severe cells.

1L SequaGel XR
NAT1162 1L
EUR 138
1L SequaGel UreaGel Concentrate
NAT1134 1L
EUR 134
1L SequaGel UreaGel-6
NAT1146 1L
EUR 126
1L SequaGel UreaGel-8
NAT1150 1L
EUR 126
1L SequaGel UreaGel Diluent
NAT1154 1L
EUR 86
sequencing system 20x50 cm
ESEQ1200-SYS ea
EUR 1535
UreaGel 29:1 System 1L Kit
NAT1128 EACH
EUR 143
REAGENT BOTTLE, 1L, PP
1500P-1L 10/pk
EUR 100
Description: Reusable Plastics; Resusable Bottles
BEAKER,1L,PLASTIC,LOW FORM,PP,6/6
1000P-1L 6/pk
EUR 63
Description: Reusable Plastics; Resuable Beakers
BEAKER,1L,PLASTIC,LOW FORM,PFA,1/6
1003P-1L 1/pk
EUR 653
Description: Reusable Plastics; Resuable Beakers
BEAKER,1L,WITH HANDLE AND SPOUT,PP,12/12
1015P-1L 12/pk
EUR 116
Description: Reusable Plastics; Resuable Beakers
SequaGel MD SSCP Kit
NAT1170 1KIT
EUR 211
SequaGel MD Heteroduplex Kit
NAT1172 EACH
EUR 221
CYLINDER,GRAD,1L,PLASTIC,SINGLE METRIC SCALE,PP,TC W/FUNNEL,1/6
3022P-1L 1/pk
EUR 161
Description: Reusable Plastics; Reusable Cylinders
100ML SequaGel Buffer
NAT1140 100ML
EUR 67
450ML SequaGel XR
NAT1160 450ML
EUR 105
VOL FLASK,1L,PLASTIC,CLASS A,PMP,24/29 TAPERED PP STOPPER,1/3
5640P-1L 1/pk
EUR 133
Description: Reusable Plastics; Reusable Volumetric Flasks
VOL FLASK,1L,PLASTIC,CLASS B,PP,24/29 TAPERED PP STOPPER,1/3
5641P-1L 1/pk
EUR 121
Description: Reusable Plastics; Reusable Volumetric Flasks
PinPoint-HR System for Platform Cell Line Generation & Retargeting (includes PIN400A-1, PIN200A-1, PIN510A-1, & PIN600A-1)
PIN400A-KIT 1 Kit
EUR 2798
  • Category: PinPoint Integrase Tools
Chymotrypsin for Sequencing grade
C4001-010 4x25ug
EUR 313
Chymotrypsin for Sequencing grade
C4001-100 100ug
EUR 286
sequencing unit 33x45 cm
ESEQ1100-SYS ea
EUR 1535
Trypin for Mass & Sequencing
T9600-025 25ug
EUR 145
Trypin for Mass & Sequencing
T9600-100 100ug
EUR 219
Trypin for Mass & Sequencing
T9600-112 12x100ug
EUR 1657
Trypin for Mass & Sequencing
T9600-400 4x100ug
EUR 651
PinPoint-FC System for Platform Cell Line Generation & Retargeting (includes PIN300A-1, FC200PA-1, PIN200A-1, PIN510A-1, & PIN600A-1)
PIN300A-KIT 1 Kit
EUR 2798
  • Category: PinPoint Integrase Tools
450ML SequaGel UreaGel Concentrate
NAT1132 450ML
EUR 105
200ML SequaGel UreaGel Buffer
NAT1142 200ML
EUR 70
450ML SequaGel UreaGel-6
NAT1144 450ML
EUR 96
450ML SequaGel UreaGel-8
NAT1148 450ML
EUR 96
450ML SequaGel UreaGel Diluent
NAT1152 450ML
EUR 75
90ML SequaGel Complete Buffer
NAT1156 90ML
EUR 66
100ML SequaGel XR Concentrate
NAT1164 100ML
EUR 107
450ML SequaGel XR Concentrate
NAT1166 450ML
EUR 301
1L HarrisHematoxylin
NAT1338 1L
EUR 123
1L Autofluor
NAT1446 1L
EUR 216
PinPoint-HR System for Platform Cell Line Generation & Retargeting of AAVS1 Safe Harbor Locus (includes PIN410A-1, GE601A-1, PIN200A-1, PIN510A-1, & PIN600A-1)
PIN410A-KIT 1 Kit
EUR 4335
  • Category: PinPoint Integrase Tools
PinPoint-HR System for Platform Cell Line Generation & Retargeting of AAVS1 Safe Harbor Locus (includes PIN410A-1, CAS601A-1, PIN200A-1, PIN510A-1, & PIN600A-1)
PIN412A-KIT 1 Kit
EUR 4335
  • Category: PinPoint Integrase Tools
DNA Library Prep Kit for IIlumina Sequencing
K1475-12 12 Rxns
EUR 480
200ML SequaGel UreaGel Complete Buffer
NAT1158 200ML
EUR 71
200ML SequaGel MD Monomer Solution
NAT1168 200ML
EUR 184
1L Opticlear Sample Kit I
NAT1494 1L
EUR 162
1L Opticlear Sample Kit II
NAT1496 1L
EUR 179
PLASTIC CLAMP, 1L
480152 1/pk
EUR 73
Description: Lab Equipment; Constant Temperature Equipment
SLINGSHOT-1L Antibody
48407-100ul 100ul
EUR 333
SLINGSHOT-1L Antibody
48407-50ul 50ul
EUR 239
SLINGSHOT-1L Antibody
abx016133-100ug 100 ug
EUR 411
  • Shipped within 5-10 working days.
SLINGSHOT-1L Antibody
abx224128-100ug 100 ug
EUR 411
  • Shipped within 5-10 working days.
Dermcidin-1L (human)
H-7316.0500 0.5mg
EUR 177
Description: Sum Formula: C210H359N57O71; CAS# [478898-18-9] net
Dermcidin-1L (human)
H-7316.1000 1.0mg
EUR 294
Description: Sum Formula: C210H359N57O71; CAS# [478898-18-9] net
1L-chiro-Inositol
GC7626-100MG 100 mg
EUR 102
1L-chiro-Inositol
GC7626-1G 1 g
EUR 269
1L Tween 20
NAT1084 1L
EUR 141
1L ProtoBlue Safe
NAT1108 1L
EUR 133
1L ProtoStain Blue
NAT1112 1L
EUR 137
1L AcrylaGel 30%
NAT1118 1L
EUR 148
1L TBE 10X
NAT1196 1L
EUR 82
1L TBE 5X
NAT1200 1L
EUR 77
1L Denaturation Solution
NAT1232 1L
EUR 85
1L Neutralization Solution
NAT1234 1L
EUR 85
1L ProtoGel (30%)
NAT1260 1L
EUR 156
1L ProtoGel (40%)
NAT1264 1L
EUR 170
1L Scotts Tapwater
NAT1342 1L
EUR 75
1L Oxosol 306
NAT1382 1L
EUR 112
Beaker Brushes, 1L
BR007-1K 1 UNIT
EUR 53.48
  • Product category: Labware/Lab Accessories/Brushes
PCR Clean Up for DNA Sequencing
BT5100 100preps
EUR 95.68
  • Product category: PCR Related/PCR Kits (Cleanup)
PCR Clean Up for DNA Sequencing
BT5101 1000Preps, 1000prep
EUR 461.08
  • Product category: PCR Related/PCR Kits (Cleanup)
1.2ML SequaGel MD SSCP Stop Solution
NAT1174 1.2ML
EUR 71
Frit Kit
FRIT-KIT 1each
EUR 124
Description: Kit to create frits in capillaries. Includes formamide, Kasil-1, Kasil-1624 and a cleaving tool.
Column Packing Kit
PACK-KIT 1pack
EUR 1035
Description: Column packing kit for pressure cells. Includes: HPREG regulator, TBNG10 tubing, CAP-75 capillary, and STRB5X2 stir bar.
Human Metallothionein- 1L, MT1L ELISA KIT
ELI-36664h 96 Tests
EUR 824
Human Metallothionein 1L(MT1L)ELISA Kit
QY-E02761 96T
EUR 361
PCR Mycoplasma Detection Kit
M034-Kit Kit
EUR 266
CELL EXPANSION BAG, 1L
91-200-85 1/pk
EUR 112
Description: Flexible Containers; Bioprocess Bags and Parts
SLINGSHOT-1L Conjugated Antibody
C48407 100ul
EUR 397
InstantBlue 1L (Instant Blue)
ISB1L 1L bottle
EUR 165
  • Shelf time: 2 years
1L DEPC Treated Water
NAT1104 1L
EUR 100
1L Bis-AcrylaGel 2%
NAT1122 1L
EUR 93
1L TAE Buffer 50X
NAT1222 1L
EUR 124
1L SSC Buffer 20X
NAT1224 1L
EUR 82
1L ProtoGel Resolving Buffer
NAT1268 1L
EUR 107
1L EDTA 0.5M Solution
NAT1282 1L
EUR 153
Cas9 Protein and T7 gRNA SmartNuclease Synthesis Kit
CAS400A-KIT 1 kit (10 rxn)
EUR 1110
  • Category: Cas9
CMV-hspCas9-T2A-Puro SmartNuclease Lentivector Plasmid + LentiStarter Packaging Kit
CASLV100PA-KIT 1 Kit
EUR 1132
  • Category: Cas9
CMV-hspCas9-EF1-GFP SmartNuclease Lentivector Plasmid + LentiStarter Packaging Kit
CASLV105PA-KIT 1 Kit
EUR 1132
  • Category: Cas9
MSCV-hspCas9-T2A-Puro SmartNuclease Lentivector Plasmid + LentiStarter Packaging Kit
CASLV120PA-KIT 1 Kit
EUR 1132
  • Category: Cas9
MSCV-hspCas9-EF1-GFP SmartNuclease Lentivector Plasmid + LentiStarter Packaging Kit
CASLV125PA-KIT 1 Kit
EUR 1132
  • Category: Cas9
Human Protein phosphatase 1L, PPM1L ELISA KIT
ELI-45425h 96 Tests
EUR 824
Bovine Protein phosphatase 1L, PPM1L ELISA KIT
ELI-36194b 96 Tests
EUR 928
Mouse Protein phosphatase 1L, Ppm1l ELISA KIT
ELI-36546m 96 Tests
EUR 865
ELISA kit for Human Metallothionein-1L (MT1L)
KTE61511-48T 48T
EUR 332
  • MT1L (Metallothionein 1L (Gene/Pseudogene)) is a Protein Coding gene. Metallothioneins have a high content of cysteine residues that bind various heavy metals
  • these proteins are transcriptionally regulated by both heavy metals and glucocorticoids.
Description: Quantitative sandwich ELISA for measuring Human Metallothionein-1L (MT1L) in samples from cell culture supernatants, serum, whole blood, plasma and other biological fluids.
ELISA kit for Human Metallothionein-1L (MT1L)
KTE61511-5platesof96wells 5 plates of 96 wells
EUR 2115
  • MT1L (Metallothionein 1L (Gene/Pseudogene)) is a Protein Coding gene. Metallothioneins have a high content of cysteine residues that bind various heavy metals
  • these proteins are transcriptionally regulated by both heavy metals and glucocorticoids.
Description: Quantitative sandwich ELISA for measuring Human Metallothionein-1L (MT1L) in samples from cell culture supernatants, serum, whole blood, plasma and other biological fluids.
ELISA kit for Human Metallothionein-1L (MT1L)
KTE61511-96T 96T
EUR 539
  • MT1L (Metallothionein 1L (Gene/Pseudogene)) is a Protein Coding gene. Metallothioneins have a high content of cysteine residues that bind various heavy metals
  • these proteins are transcriptionally regulated by both heavy metals and glucocorticoids.
Description: Quantitative sandwich ELISA for measuring Human Metallothionein-1L (MT1L) in samples from cell culture supernatants, serum, whole blood, plasma and other biological fluids.
Multiplex gRNA Kit + EF1-T7-hspCas9-H1-gRNA linearized SmartNuclease vector
CAS700A-KIT 10 rxn
EUR 1132
  • Category: Cas9
Multiplex gRNA Kit + CAG-T7-hspCas9-H1-gRNA linearized SmartNuclease vector
CAS720A-KIT 10 rxn
EUR 1132
  • Category: Cas9
Multiplex gRNA Kit + CMV-T7-hspCas9-H1-gRNA linearized SmartNuclease vector
CAS740A-KIT 10 rxn
EUR 1132
  • Category: Cas9
T7 gRNA SmartNuclease Synthesis Kit (includes CAS510A-1 & T7 IVT synthesis reagents)
CAS510A-KIT 1 Kit
EUR 805
  • Category: Cas9

We also identified some of the genes responsible for the change in the score DGIE occur during cell differentiation is based on three single-cell dataset real. Our results show that single-cell analysis is based on inference network coupled with quantitative calculations can reveal key transcriptional regulators involved in cell differentiation and disease progression.

Leave A Comment