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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 UreaGel-6 - 1L
NAT1146 1L
EUR 152.55

1L SequaGel UreaGel-8 - 1L
NAT1150 1L
EUR 152.55

1L SequaGel UreaGel Diluent - 1L
NAT1154 1L
EUR 72.9

1L SequaGel UreaGel Concentrate - 1L
NAT1134 1L
EUR 160.65

SequaGel MD SSCP Kit - 1KIT
NAT1170 1KIT
EUR 318.6

450ML SequaGel XR - 450ML
NAT1160 450ML
EUR 112.05

pOET Sequencing Primers
GWB-200100 2 x 100 ul Ask for price

SequaGel MD Heteroduplex Kit - EACH
NAT1172 EACH
EUR 337.5

sequencing unit 33x45 cm
ESEQ1100-SYS ea
EUR 1842

100ML SequaGel Buffer - 100ML
NAT1140 100ML
EUR 36.45

Trypin for Mass & Sequencing
T9600-025 25ug
EUR 174

Trypin for Mass & Sequencing
T9600-100 100ug
EUR 262.8

Trypin for Mass & Sequencing
T9600-112 12x100ug
EUR 1988.4

Trypin for Mass & Sequencing
T9600-400 4x100ug
EUR 781.2

Sequencing Grade Chymotrypsin
RE013 100ug
EUR 309

Sequencing Grade V8 Protease
RE014 50ug
EUR 209

EpiNext Bisulfite Sequencing Kit (Illumina)
P-1056
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  • 24 Reactions
  • 12 Reactions
  • 24 Reactions

TNM Sequencing Primers for SE
TMS002-C1-1rxn 1 rxn
EUR 115

TNM Sequencing Primers for PE
TMS002-C2-1rxn 1 rxn
EUR 143.88

Chymotrypsin for Sequencing grade
C4001-010 4x25ug
EUR 375.6

Chymotrypsin for Sequencing grade
C4001-100 100ug
EUR 343.2

Sequencing Grade Modified Trypsin
RE012 100ug
EUR 229

450ML SequaGel UreaGel-6 - 450ML
NAT1144 450ML
EUR 95.85

450ML SequaGel UreaGel-8 - 450ML
NAT1148 450ML
EUR 95.85

Oligo, Sequencing Primer, SK (17mer)
MBS634188-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, SK (17mer)
MBS634188-5x0033mg 5x0.033mg
EUR 1235

Oligo, Sequencing Primer, KS (17mer)
MBS634192-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, KS (17mer)
MBS634192-5x0033mg 5x0.033mg
EUR 1235

Oligo, Sequencing Primer, SK (20mer)
MBS634219-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, SK (20mer)
MBS634219-5x0033mg 5x0.033mg
EUR 1240

Oligo, Sequencing Primer, T3 (17mer)
MBS634243-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, T3 (17mer)
MBS634243-5x0033mg 5x0.033mg
EUR 1235

Oligo, Sequencing Primer, T7 (17mer)
MBS634247-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, T7 (17mer)
MBS634247-5x0033mg 5x0.033mg
EUR 1235

Oligo, Sequencing Primer, KS (19mer)
MBS634259-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, KS (19mer)
MBS634259-5x0033mg 5x0.033mg
EUR 1235

Oligo, Sequencing Primer, T3 (20mer)
MBS634261-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, T3 (20mer)
MBS634261-5x0033mg 5x0.033mg
EUR 1240

PCR Clean Up for DNA Sequencing
BT5100 100preps
EUR 114.82

PCR Clean Up for DNA Sequencing
BT5101 1000Preps, 1000prep
EUR 553.3

ACES Sequencing Buffer 10X, pH 7.7
21420000-1 1 L
EUR 138.62

ACES Sequencing Buffer 10X, pH 7.7
21420000-2 4 L
EUR 456.17

DNA Library Prep Kit for IIlumina Sequencing
K1475-12 12 Rxns
EUR 576

Sequencing Grade Carboxypeptidase B
RE011 100ug
EUR 99

200ML SequaGel UreaGel Buffer - 200ML
NAT1142 200ML
EUR 41.85

90ML SequaGel Complete Buffer - 90ML
NAT1156 90ML
EUR 35.1

100ML SequaGel XR Concentrate - 100ML
NAT1164 100ML
EUR 116.1

450ML SequaGel XR Concentrate - 450ML
NAT1166 450ML
EUR 494.1

450ML SequaGel UreaGel Diluent - 450ML
NAT1152 450ML
EUR 52.65

TBE-Buffer 5X for DNA Sequencing
40121072-1 100 mL
EUR 26.54

TBE-Buffer 5X for DNA Sequencing
40121072-2 500 mL
EUR 44.84

TBE-Buffer 5X for DNA Sequencing
40121072-3 1 L
EUR 72.29

TBE-Buffer 5X for DNA Sequencing
40121072-4 4 L
EUR 192.14

450ML SequaGel UreaGel Concentrate - 450ML
NAT1132 450ML
EUR 112.05

Bovine Trypsin Purified Sequencing Grade
IBOTRYSEQ100UG each
EUR 148
Description: Bovine Trypsin Purified Sequencing Grade

Bovine Trypsin Purified Sequencing Grade
IBOTRYSEQ1MG each
EUR 765
Description: Bovine Trypsin Purified Sequencing Grade

Bovine Trypsin Purified Sequencing Grade
IBOTRYSEQ400UG each
EUR 419
Description: Bovine Trypsin Purified Sequencing Grade

Bovine Trypsin Purified Sequencing Grade
MBS136298-01mg 0.1mg
EUR 255

Bovine Trypsin Purified Sequencing Grade
MBS136298-04mg 0.4mg
EUR 540

Bovine Trypsin Purified Sequencing Grade
MBS136298-1mg 1mg
EUR 935

Bovine Trypsin Purified Sequencing Grade
MBS136298-5x1mg 5x1mg
EUR 4010

200ML SequaGel MD Monomer Solution - 200ML
NAT1168 200ML
EUR 264.6

1.2ML SequaGel MD SSCP Stop Solution - 1.2ML
NAT1174 1.2ML
EUR 44.55

MagaDye™ 4 Color Sanger Sequencing Terminator Kit
17068 5 nmoles
EUR 2091

Oligo, Sequencing Primer, T7 Universal (20mer)
MBS634194-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, T7 Universal (20mer)
MBS634194-5x0033mg 5x0.033mg
EUR 1240

Oligo, Sequencing Primer, SP6 Promoter (19mer)
MBS634260-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, SP6 Promoter (19mer)
MBS634260-5x0033mg 5x0.033mg
EUR 1235

200ML SequaGel UreaGel Complete Buffer - 200ML
NAT1158 200ML
EUR 44.55

Trifluoroacetic Acid (TFA) for HPLC & Sequencing, 99.9%
23947 10 x1 ml
EUR 165.03
Description: Part A

Oligo, Sequencing Primer, Lambda gt11, Reverse (24mer)
MBS634120-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, Lambda gt11, Reverse (24mer)
MBS634120-5x0033mg 5x0.033mg
EUR 1245

Oligo, Sequencing Primer, Lambda gt10, Reverse (31mer)
MBS634167-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, Lambda gt10, Reverse (31mer)
MBS634167-5x0033mg 5x0.033mg
EUR 1245

Oligo, Sequencing Primer, Lambda gt11, Forward (24mer)
MBS634252-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, Lambda gt11, Forward (24mer)
MBS634252-5x0033mg 5x0.033mg
EUR 1245

Oligo, Sequencing Primer, Lambda gt10, Forward (27mer)
MBS634255-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, Lambda gt10, Forward (27mer)
MBS634255-5x0033mg 5x0.033mg
EUR 1240

Bovine Trypsin Purified Sequencing Grade Lyophilized
IBOTRYSEQLY100UG each
EUR 130
Description: Bovine Trypsin Purified Sequencing Grade Lyophilized

Bovine Trypsin Purified Sequencing Grade Lyophilized
IBOTRYSEQLY1MG each
EUR 640
Description: Bovine Trypsin Purified Sequencing Grade Lyophilized

Bovine Trypsin Purified Sequencing Grade Lyophilized
IBOTRYSEQLY400UG each
EUR 344
Description: Bovine Trypsin Purified Sequencing Grade Lyophilized

Bovine Trypsin Purified Sequencing Grade Lyophilized
MBS136299-01mg 0.1mg
EUR 235

Bovine Trypsin Purified Sequencing Grade Lyophilized
MBS136299-04mg 0.4mg
EUR 465

Bovine Trypsin Purified Sequencing Grade Lyophilized
MBS136299-1mg 1mg
EUR 795

Bovine Trypsin Purified Sequencing Grade Lyophilized
MBS136299-5x1mg 5x1mg
EUR 3400

Oligo, Sequencing Primer, pBR322 (EcoR I), Clockwise (16mer)
MBS634158-0033mg 0.033mg
EUR 305

Oligo, Sequencing Primer, pBR322 (EcoR I), Clockwise (16mer)
MBS634158-5x0033mg 5x0.033mg
EUR 1230

Oligo, Sequencing Primer, pBR322 (BamH I), Clockwise (20mer)
MBS634234-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, pBR322 (BamH I), Clockwise (20mer)
MBS634234-5x0033mg 5x0.033mg
EUR 1240

Oligo, Sequencing Primer, pBR322 (Pst I), Counterclockwise (16mer)
MBS634143-0033mg 0.033mg
EUR 305

Oligo, Sequencing Primer, pBR322 (Pst I), Counterclockwise (16mer)
MBS634143-5x0033mg 5x0.033mg
EUR 1230

Oligo, Sequencing Primer, pBR322 (BamH I), Counterclockwise (16mer)
MBS634262-0033mg 0.033mg
EUR 305

Oligo, Sequencing Primer, pBR322 (BamH I), Counterclockwise (16mer)
MBS634262-5x0033mg 5x0.033mg
EUR 1230

Genorise® Customized PCR primers for cloning and sequencing
GR108023 2 nmol
EUR 65

Oligo, Sequencing Primer, pBR322 (Hind III), Counterclockwise (16mer)
MBS634154-0033mg 0.033mg
EUR 305

Oligo, Sequencing Primer, pBR322 (Hind III), Counterclockwise (16mer)
MBS634154-5x0033mg 5x0.033mg
EUR 1230

Oligo, Sequencing Primer, M13 Reverse (16mer) [5'-AAC AGC TAT GAC CAT G-3']
MBS634131-0033mg 0.033mg
EUR 305

Oligo, Sequencing Primer, M13 Reverse (16mer) [5'-AAC AGC TAT GAC CAT G-3']
MBS634131-5x0033mg 5x0.033mg
EUR 1230

Bovine Alpha Chymotrypsin 3X Crystallized TLCK Treated Sequencing Grade
IBOCHYTLCKSG100UG each
EUR 297
Description: Bovine Alpha Chymotrypsin 3X Crystallized TLCK Treated Sequencing Grade

Bovine Alpha Chymotrypsin 3X Crystallized TLCK Treated Sequencing Grade
MBS136223-01mg 0.1mg
EUR 400

Bovine Alpha Chymotrypsin 3X Crystallized TLCK Treated Sequencing Grade
MBS136223-5x01mg 5x0.1mg
EUR 1605

Oligo, Sequencing Primer, M13 (-20) Forward (17mer) [5'-GTA AAA CGA CGG CCA GT-3']
MBS634146-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, M13 (-20) Forward (17mer) [5'-GTA AAA CGA CGG CCA GT-3']
MBS634146-5x0033mg 5x0.033mg
EUR 1235

Oligo, Sequencing Primer, M13 Reverse (19mer) [5'-GGA AAC AGC TAT GAC CAT G-3']
MBS634148-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, M13 Reverse (19mer) [5'-GGA AAC AGC TAT GAC CAT G-3']
MBS634148-5x0033mg 5x0.033mg
EUR 1235

Bacteria-Derived V8 Protease (Endoprotease Glu-C) Sequencing Grade Lyophilized
IBCTV8SEQLY250UG each
EUR 784
Description: Bacteria-Derived V8 Protease (Endoprotease Glu-C) Sequencing Grade Lyophilized

Bacteria-Derived V8 Protease (Endoprotease Glu-C) Sequencing Grade Lyophilized
IBCTV8SEQLY50UG each
EUR 304
Description: Bacteria-Derived V8 Protease (Endoprotease Glu-C) Sequencing Grade Lyophilized

Bacteria-Derived Clostripain (Endoproteinase-Arg-C) Sequencing Grade Purified
IBCTCLOSGPF10UG each
EUR 165
Description: Bacteria-Derived Clostripain (Endoproteinase-Arg-C) Sequencing Grade Purified

Bacteria-Derived Clostripain (Endoproteinase-Arg-C) Sequencing Grade Purified
MBS136171-01mg 0.1mg
EUR 270

Bacteria-Derived Clostripain (Endoproteinase-Arg-C) Sequencing Grade Purified
MBS136171-5x001mg 5x0.01mg
EUR 1035

SEPTA MAT, FOR 96 WELL PCR PLATES, SILICONE, GREY, NONSTERILE, FOR ABI MULTI-CAPILLARY SEQUENCING INSTRUMENTS, BULK
AM-96-SEPTA-3100 10/pk
EUR 639.6
Description: Sealing Products; Sealing mats - Axygen

UreaGel 29:1 System 1L Kit - EACH
NAT1128 EACH
EUR 187.65

ACES™ Signal Sequence Kit
0148-2 kit
EUR 198.7

Kinesis Filtration System 300ml/1L; replacement Filter Flask - EACH
FIL1005 EACH
EUR 124.85

Watershed System Kit
M-WS180320-1 1 KIT
EUR 9296
Description: Watershed System Kit

Human G- rich sequence factor 1, GRSF1 ELISA KIT
ELI-39072h 96tests
EUR 696

Mouse G- rich sequence factor 1, Grsf1 ELISA KIT
ELI-42875m 96tests
EUR 736

Mouse G-Rich Sequence Factor 1 (GRSF1) ELISA Kit
abx389463-96tests 96 tests
EUR 1093.2

Human G-Rich Sequence Factor 1 (GRSF1) ELISA Kit
abx384974-96tests 96 tests
EUR 1093.2

Human G-rich sequence factor 1, GRSF1 ELISA Kit
MBS9332726-10x96StripWells 10x96-Strip-Wells
EUR 6725

Human G-rich sequence factor 1, GRSF1 ELISA Kit
MBS9332726-48StripWells 48-Strip-Wells
EUR 550

Human G-rich sequence factor 1, GRSF1 ELISA Kit
MBS9332726-5x96StripWells 5x96-Strip-Wells
EUR 3420

Human G-rich sequence factor 1, GRSF1 ELISA Kit
MBS9332726-96StripWells 96-Strip-Wells
EUR 765

Mouse G-rich sequence factor 1, GRSF1 ELISA Kit
MBS9341616-10x96StripWells 10x96-Strip-Wells
EUR 6725

Mouse G-rich sequence factor 1, GRSF1 ELISA Kit
MBS9341616-48StripWells 48-Strip-Wells
EUR 550

Mouse G-rich sequence factor 1, GRSF1 ELISA Kit
MBS9341616-5x96StripWells 5x96-Strip-Wells
EUR 3420

Mouse G-rich sequence factor 1, GRSF1 ELISA Kit
MBS9341616-96StripWells 96-Strip-Wells
EUR 765

human similar to cDNA sequence BC027382 ELISA Kit
YLA2833HU-48T 48T Ask for price

human similar to cDNA sequence BC027382 ELISA Kit
YLA2833HU-96T 96T Ask for price

Human similar to cDNA sequence BC027382 ELISA Kit
GA-E1905HM-48Tests 48 Tests Ask for price

Human similar to cDNA sequence BC027382 ELISA Kit
GA-E1905HM-96Tests 96 Tests
EUR 388

Human similar to cDNA sequence BC027382 ELISA Kit
GA-E1905HM-48T 48T
EUR 346.8

Human similar to cDNA sequence BC027382 ELISA Kit
GA-E1905HM-96T 96T
EUR 559.2

Human similar to cDNA sequence BC027382 ELISA Kit
QY-E02390 96T
EUR 433.2

Human similar to cDNA sequence BC027382 ELISA Kit
MBS9301278-10x96StripWells 10x96-Strip-Wells
EUR 6725

Human similar to cDNA sequence BC027382 ELISA Kit
MBS9301278-48StripWells 48-Strip-Wells
EUR 550

Human similar to cDNA sequence BC027382 ELISA Kit
MBS9301278-5x96StripWells 5x96-Strip-Wells
EUR 3420

Human similar to cDNA sequence BC027382 ELISA Kit
MBS9301278-96StripWells 96-Strip-Wells
EUR 765

human similar to cDNA sequence BC027382 ELISA Kit
201-12-1889 96 tests
EUR 528
Description: A quantitative ELISA kit for measuring Human in samples from biological fluids.

OVA sequence (323-336)
TP1612-10mg 10mg Ask for price
Description: OVA sequence (323-336)

OVA sequence (323-336)
TP1612-1g 1g Ask for price
Description: OVA sequence (323-336)

OVA sequence (323-336)
TP1612-1mg 1mg Ask for price
Description: OVA sequence (323-336)

OVA sequence (323-336)
TP1612-50mg 50mg Ask for price
Description: OVA sequence (323-336)

OVA sequence (323-336)
TP1612-5mg 5mg Ask for price
Description: OVA sequence (323-336)

OVA sequence (323-336)
MBS5801532-INQUIRE INQUIRE Ask for price

Single Cell Sequence Specific Amplification Kit
P621-01 200 rxn
EUR 435

Human GC- rich sequence DNA- binding factor, TCF9 ELISA KIT
ELI-27490h 96tests
EUR 696

Mouse GC- rich sequence DNA- binding factor, Tcf9 ELISA KIT
ELI-12525m 96tests
EUR 736

Human Myeloid cell leukemia sequence 1 (MCL1) ELISA Kit
YLA3907HU-48T 48T Ask for price

Human Myeloid cell leukemia sequence 1 (MCL1) ELISA Kit
YLA3907HU-96T 96T Ask for price

Human MCL1(Myeloid Cell Leukemia Sequence 1) ELISA Kit
RE2013H-48wells 48 wells
EUR 125.55

Human MCL1(Myeloid Cell Leukemia Sequence 1) ELISA Kit
RE2013H-96wells 96 wells
EUR 179.55

Human MCL1(Myeloid Cell Leukemia Sequence 1) ELISA Kit
RE2013H-48wellsplate 48 wells plate
EUR 126

Human MCL1(Myeloid Cell Leukemia Sequence 1) ELISA Kit
RE2013H-96wellsplate 96 wells plate
EUR 180

Rat Malignant T cell-amplified sequence 1 ELISA Kit
MBS2882544-10x96StripWells 10x96-Strip-Wells
EUR 4080

Rat Malignant T cell-amplified sequence 1 ELISA Kit
MBS2882544-48StripWells 48-Strip-Wells
EUR 390

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.

MarK

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