Supplementary Figure 1

Size: px
Start display at page:

Download "Supplementary Figure 1"

Transcription

1 Supplementary Figure 1 Supplementary Fig. 1: Quality assessment of formalin-fixed paraffin-embedded (FFPE)-derived DNA and nuclei. (a) Multiplex PCR analysis of unrepaired and repaired bulk FFPE gdna from Cases 1-4. (b) Multiplex PCR results from three FFPE samples (Samples A, B and C) considered overly degraded (two multiplex PCR bands) and not sequenced in this study. Sample D is an FFPE sample that presented with heavy immune infiltrate (main text), and was not further analyzed. (c) Multiplex PCR of gdna from matching frozen samples of Cases 1-4. (d) Multiplex PCR of FFPE (repaired) and frozen (unrepaired) gdna from MCF-7 and CAMA-1 cells. DCIS: ductal carcinoma in situ, IDC: Invasive ductal carcinoma. Rep: repaired, UnRep: unrepaired. (e) FFPE and frozen single nuclei preparations are enriched for intact nuclei: representative confocal micrographs of DAPIstained FFPE (left) and frozen (right) nuclei. A minority of nuclei was non-intact (green arrows). Micrographs were taken from Case 1 (tumor) and Case 2 (tumor and normal/ lymph node), with a 63x optical lens and 5.2x digital zoom (~330x magnification). (f) Size distribution profiles of whole-genome amplified (WGA) unrepaired and repaired single FFPE nuclei DNA of Cases 1-4, and WGA frozen nuclei DNA of Case 1. Representative agarose gel-based WGA profiles. Slight differences in molecular weight of amplicons are noted after DNA restoration for all FFPE nuclei; no difference is observed in frozen nuclei of Case 1. (g) Singlenucleus DNA repair increases the relative amount of template DNA available for WGA in repaired FFPE nuclei relative to unrepaired nuclei as defined by Ct values from real-time SYBR Green WGA reactions of diploid (2N) nuclei (Frozen unrepaired diploid, n=8; FFPE unrepaired diploid, n=10; FFPE repaired diploid, n=20). Repaired triploid (3N) frozen and FFPE nuclei are included in the plot for comparison purposes only (Frozen repaired triploid, n=5; FFPE repaired triploid, n=5). ****P < ; Mann-Whitney U test.

2 Supplementary Figure 2 Supplementary Fig. 2: Qualitative concordance of cytometric parameters between formalin-fixed paraffinembedded (FFPE) and frozen nuclei preparations. (a) Case 1 (TNBC) FFPE and frozen single nuclei. (b) MCF-7 and CAMA-1 breast cancer cell line FFPE and frozen nuclei. (c) Case 2 FFPE and frozen nuclei derived from ductal carcinoma in situ (DCIS) and invasive breast cancer. Multigraph images show nine cytometric parameters of single FFPE and frozen nuclei. Parameters analyzed are: Side Scatter-Area/Width/Height (SSC-A, SSC-W, SSC-H), Forward Scatter Area/Width/Height (FSC-A, FSC-W, FSC-H) and DAPI-Area/Width/Height (DAPI-A, DAPI-W, DAPI-H).

3 Supplementary Figure 3 Supplementary Fig. 3: Single-cell and bulk DNA copy number analysis of Case 1. (a) Diploid nuclei of Case 1 (TNBC) displayed genomically normal ( flat ) profiles: representative examples of genome-wide single-cell copy number (CN) profiles from single formalin-fixed paraffin-embedded (FFPE) diploid nuclei, single frozen diploid nuclei and their respective bulk profiles (~100,000 nuclei) obtained through low-pass whole-genome sequencing. (b) CN profiles derived from bulk tumor analysis from Case 1 corroborate the results obtained from single nuclei sequencing analysis: bulk sequencing profiles of nuclei (~100,000) derived from the 3N peak display highly rearranged genomes that are similar to those of single nuclei (FFPE and frozen). CN values shown are rounded to the closest integer. (c) CN profile of bulk tumor nuclei from Case 1 displays non-integer CN values on chromosome 8 indicative of sub-clonality. The sub-clonality is corroborated by single nuclei data. (d) High bin-to-bin variability in a subset of unrepaired FFPE cells of Case 1: representative CN profiles of a noisy unrepaired FFPE nucleus in comparison to a representative CN profile observed for the vast majority of repaired nuclei. Normalized read counts for each bin are indicated in grey. Blue line is the estimated CN. (e) Repaired FFPE nuclei display improved qualitative sequencing parameters compared to unrepaired nuclei: unrepaired normal nuclei of Case 1 display high bin-to-bin variance/noise, expressed as the Sum-of-square error (error bars, standard deviation of mean). Nuclei repair improves the variance. (f) Lorenz curves of coverage uniformity (top) and Lowess fit of GC-content with respect to Log 2 -normalized bin counts (bottom) for unrepaired (left) and repaired (right) FFPE nuclei. In the overlay images, different colors indicate different nuclei. Straight line (red arrow) with slope 1 in Lorenz curves denotes perfect uniformity.

4 Supplementary Figure 4 Supplementary Fig. 4: Validation of single-cell copy number (CN) analysis using breast cancer cell lines. (a) Cytometric distributions of formalin-fixed paraffin-embedded (FFPE) and frozen MCF-7 and CAMA-1 single cells, and pre-defined MCF7/CAMA-1 cell mixes (1:1 and 4:1). (b) Hierarchical clustering heatmap of all FFPE/frozen MCF-7 and CAMA-1 nuclei (FFPE CAMA-1, n=67; Frozen CAMA-1, n=57; FFPE MCF-7, n=125; Frozen MCF-7, n=135). Phenobar indicates MCF-7 and CAMA-1 cells. Chr: chromosome, Sc: single cell. Hierarchical clustering heatmap trees were constructed using CN profiles of individual cells using Manhattan distance and Ward s method. (c) Bin-to-bin variance (expressed as the Sum-of-square error) of FFPE (repaired)/frozen MCF-7 and CAMA-1 single cells (error bars, standard deviation of mean). (d) Concordance between the CN profiles obtained from FFPE (repaired)/frozen MCF-7 and CAMA-1 single cells and the respective CN profiles obtained through bulk sequencing (error bars, standard deviation of mean). (e) Close-up views illustrating examples of sub-clonal CN alterations in Chr10 and Chr7 (p22.3-p14.3) identified in single cells (FFPE and frozen) in comparison with the respective profiles obtained through bulk sequencing; the not rounded CN value of the alteration in the bulk lays in between the integer CN values of both subclones in each region depicted. (f) The real, experimentally derived MCF-7:CAMA-1 ratios as defined by the CN profiles are consistent with the theoretical mixing ratios: hierarchical clustering heatmaps of all pre-defined FFPE and frozen mixes of single cells (96 cells per experiment were analyzed). The real percentages of each cell line in the mix as defined by CN profiling are indicated. Chr: chromosome, Sc: single cell. Hierarchical clustering heatmap trees were constructed using CN profiles of individual cells using Manhattan distance and Ward s method.

5 Supplementary Figure 5 Supplementary Fig. 5: Case 2 frozen tissue ploidy profiles. (a) Frozen tissue from both the ductal carcinoma in situ (DCIS) and the invasive carcinoma components display diploid (2N) and triploid (~3N) distributions. (b) Hierarchical clustering heatmap of the 2N distribution nuclei from the frozen DCIS component (n=41), constructed using the copy number (CN) profiles of individual cells using Manhattan distance and Ward s method. Nuclei from the 2N distribution display normal/ flat CN profiles. Chr: chromosome, Sc: single cell.

6 Supplementary Figure 6 Supplementary Fig. 6: High bin-to-bin variability, poor uniformity of coverage and variable GC-bias in unrepaired formalin-fixed paraffin-embedded (FFPE) cells from Case 2. (a) Representative copy number (CN) profiles of an unrepaired FFPE nucleus in comparison to a typical CN profile observed in the vast majority of repaired nuclei. Normalized read counts for each bin are indicated in grey. The blue line is the estimated CN. (b) Lorenz curves of coverage uniformity (top) and Lowess fit of GC-content with respect to Log 2 -normalized bin counts (bottom) for unrepaired (left) and repaired (right) nuclei isolated from FFPE material. In the overlay images, different colors indicate different nuclei. Straight line (red arrow) with slope 1 in Lorenz curves denotes perfect uniformity. (c) Bulk DNA CN profiling of Case 2: CN profiles of the frozen ductal carcinoma in situ (DCIS), the frozen invasive breast cancer and the FFPE DCIS nuclei derived from low-pass whole-genome sequencing data. CN values of the tumor bulks were rounded to the closest integer. FFPE invasive breast cancer tumor bulk was not sequenced due to insufficient genomic DNA material. Red arrows point to the truncal CN alterations found in all FFPE/frozen single cells. Note that the presumable truncal 11q loss was only detected in the FFPE DCIS bulk and not in the frozen bulks.

7 Supplementary Figure 7 Supplementary Fig. 7: Proposed evolutionary models for the progression from ductal carcinoma in situ (DCIS) to invasive breast cancer. (a) Proposed model for Case 2 Parallel progression model. (b) Proposed model for Case 3 Bottle-neck progression model.

8 Supplementary Figure 8 Supplementary Fig 8: Formalin-fixed paraffin-embedded (FFPE) and frozen single nuclei from Case 3 display similar copy number (CN) profiles and share clonal alterations. (a) Ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) CN profiles derived from bulk frozen whole-exome sequencing data. Not rounded CN values are shown. Red arrows point to clonal CN alterations. (b) Examples of genome-wide single-cell CN profiles from FFPE and frozen single cells. (c) Zoomed in views of CN alterations identified in single FFPE and frozen nuclei on Chr11 and Chr17. Each colored line represents a single cell. (d) Representative CN profiles of Case 3 subclones: DC-1, DC-2, DC-3, and DC-4 annotation refers to identified DCIS subclones. IC-1 and IC-2 annotation refers to identified invasive subclones (See Fig. 3). Red and blue arrows point to clonal and subclonal CN alterations, respectively. FGFR1, fibroblast growth factor receptor 1. CCND1, cyclin D1. PTEN, phosphatase and tensin homolog. Rb1, RB transcriptional corepressor 1. TP53, tumor protein p53.

9 Supplementary Figure 9 Supplementary Fig. 9: Validation of single-cell sequencing findings of Case 3 using fluorescence in situ hybridization (FISH). (a) Scanning micrographs of sequential H&E (left) and DAPI (right) stained sections of two tissue fragments of Case 3 showing synchronous ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). Contoured regions indicate the DCIS (yellow) and the IDC (green), and the regions where specific subclones were found (10x magnification). (b) Close-up micrographs of the 3-color probe panel DNA-FISH analysis illustrating specific sub-clonal alterations, which define the sub-clones identified by single-cell sequencing analysis. Notably, the CCND1 amplification in the DCIS and IDC and the PTEN homozygous deletion in the IDC were clonal by both methods, and the frequencies of each subclone within the DCIS and IDC as assessed by FISH (information described on the left) were similar (i.e., not statistically different) to those defined by single cell sequencing (Fig. 4d). CCND1 (green), SRC (red), GNAQ (orange), PTEN (red) and OCIAD1 (orange) FISH probes were used as indicated. DAPI was used for nuclei staining (blue). DAPI (only) and FISH micrographs were taken with 10x and 63x magnification, respectively. CCND1, cyclin D1; GNAQ, G protein subunit alpha q; OCIAD1, OCIA domain containing 1; PTEN, phosphatase and tensin homolog; SRC, SRC proto-oncogene, non-receptor tyrosine kinase.

10 Supplementary Figure 10 Supplementary Fig. 10. Phylogenetic tracing based on whole-exome sequencing (WES) reveals a progression model (bottle-neck progression) similar to the one extrapolated from single nuclei analysis. (a) Genome wide copy number (CN) profiles of Case 3 DCIS and IDC samples obtained from WES analysis using FACETS (Shen et al, Reference 42). (b) Cancer Cell Fraction (CCF) of single nucleotide variants (SNVs) defined using the algorithm ABSOLUTE (Carter et al, Reference 11). (c) and (d) Phylogenetic trees constructed using maximum parsimony optimality criterion for CN (c) and SNVs (d). WES was performed on two sets of samples (plus matching normal) for each component of Case 3, DCIS-1/IDC-1 (using NimbleGen SeqCap EZ Human Exome Library v2.0 capture) and DCIS-2/IDC-2 (using SureSelect Human All Exon v4 capture) (see Online Methods). DCIS, ductal carcinoma in situ; IDC, invasive ductal carcinoma.

11 Supplementary Table 1. Summary of cells sequenced in this study and statistical analyses. sequenced per case and per cell line FFPE Frozen Peak 2N ~3N 2N ~3N Case 1 Repaired Unrepaired Case 2 Case 3 Case 4 MCF-7/CAMA-1 FFPE Frozen Component/Peak DCIS(~3N) IDC(~3N) DCIS(~3N) IDC(~3N) 2N Repaired Unrepaired FFPE Frozen Component DCIS(2N) IDC(2N) DCIS(2N) IDC(2N) Repaired FFPE Frozen Component/Peak DCIS(~4N) IDC(~4N) DCIS(~4N) IDC(~4N) Repaired Unrepaired FFPE Frozen Mix 1:1 mix 4:1 mix 1:1 mix 4:1 mix Repaired Unrepaired Spearman correlation of cell line single nuclei profiles with bulk profile MCF-7 MCF-7 FFPE Frozen Spearman correlation P-value < 2.2e-16 < 2.2e-16 Spearman correlation P-value < 2.2e-16 < 2.2e-16 Down-sampling statistics Original # of cells* minimum** mean** median** FFPE (4:1 Mix) Frozen (4:1 Mix) * Refers to the actual number of CAMA-1 profiles detected from the 96 single nuclei sequenced ** Minimum, mean and median statistics are derived from the analysis of 10,000 down-sampling experiments

12 Supplementary Table 2. Quantification of fluorescence in situ hybridization (FISH) data of Case 3. Clone Copy number by single cell sequencing DC1 CCND1 amplification, 20q (SRC) gain. 9q (GNAQ) unaltered, PTEN unaltered, 4p (OCIAD1) unaltered Panel 1 Panel 2 Panel 3 Panel 4 CCND1 SRC GNAQ CCND1 PTEN OCIAD1 CCND1 PTEN Cen10 CCND1 Cen4 OCIAD1 counted Mean amp amp amp amp Min Max large clusters >2 copies copies copy copy Clone DC2 Copy number by single cell CCND1 amplification, 20q (SRC) gain, 9q (GNAQ) loss, PTEN unaltered, 4p (OCIAD1) unaltered sequencing Panel 1 Panel 2 Panel 3 Panel 4 SRC PTEN PTEN Cen4 CCND1 GNAQ CCND1 OCIAD1 CCND1 Cen10 CCND1 OCIAD1 counted not performed not performed Mean amp amp Min Max large clusters >2 copies copies copy copy Clone DC3/DC4 Copy number by CCND1 amplification, 20q (SRC) unaltered 9q (GNAQ) unaltered, PTEN hemizygous loss, 4p (OCIAD1) single cell unaltered sequencing Panel 1 Panel 2 Panel 3 Panel 4 SRC PTEN PTEN Cen4 CCND1 GNAQ CCND1 OCIAD1 CCND1 Cen10 CCND1 OCIAD1 counted Mean amp amp amp amp Min Max large clusters >2 copies copies copy copy Clone IC1 Copy number by CCND1 amplification, 20q (SRC) unaltered, 9q (GNAQ) unaltered, PTEN homozygous loss, 4p (OCIAD1) single cell unaltered sequencing Panel 1 Panel 2 Panel 3 Panel 4 SRC PTEN PTEN Cen4 CCND1 GNAQ CCND1 OCIAD1 CCND1 Cen10 CCND1 OCIAD1 counted Mean amp amp amp amp Min Max large clusters >2 copies copies copy copy Clone IC2 Copy number by single cell CCND1 amplification, 20q (SRC) unaltered, 9q (GNAQ) unaltered, PTEN homozygous loss, 4p (OCIAD1) loss sequencing Panel 1 Panel 2 Panel 3 Panel 4 SRC PTEN PTEN Cen4 CCND1 GNAQ CCND1 OCIAD1 CCND1 Cen10 CCND1 OCIAD1 counted Mean amp amp amp amp Min Max large clusters >2 copies copies copy copy Normal tissue Normal 1 Normal 2 Normal 3 panel 1 CCND1 SRC GNAQ CCND1 SRC GNAQ CCND1 SRC GNAQ counted Mean Min Max large clusters >2 copies copies copy copy Normal 1 Normal 2 Normal 3 Normal tissue panel 2 CCND1 PTEN OCIAD1 CCND1 PTEN OCIAD1 CCND1 PTEN OCIAD1 counted Mean Min Max large clusters >2 copies copies copy copy Normal tissue Normal 1 Normal 2 Normal 3 panel 3 CCND1 PTEN Cen10 CCND1 PTEN Cen10 CCND1 PTEN Cen10 counted Mean Min Max large clusters >2 copies copies copy copy Normal tissue Normal 1 Normal 2 Normal 3 panel 4 CCND1 Cen4 OCIAD1 CCND1 Cen4 GNAQ CCND1 Cen4 GNAQ counted Mean Min Max large clusters >2 copies copies copy copy AMP, amplification

13 Supplementary Table 3. Primers, adapters, and barcode sequences.

Abstract. Optimization strategy of Copy Number Variant calling using Multiplicom solutions APPLICATION NOTE. Introduction

Abstract. Optimization strategy of Copy Number Variant calling using Multiplicom solutions APPLICATION NOTE. Introduction Optimization strategy of Copy Number Variant calling using Multiplicom solutions Michael Vyverman, PhD; Laura Standaert, PhD and Wouter Bossuyt, PhD Abstract Copy number variations (CNVs) represent a significant

More information

Lentiviral Delivery of Combinatorial mirna Expression Constructs Provides Efficient Target Gene Repression.

Lentiviral Delivery of Combinatorial mirna Expression Constructs Provides Efficient Target Gene Repression. Supplementary Figure 1 Lentiviral Delivery of Combinatorial mirna Expression Constructs Provides Efficient Target Gene Repression. a, Design for lentiviral combinatorial mirna expression and sensor constructs.

More information

Interactive analysis and quality assessment of single-cell copy-number variations

Interactive analysis and quality assessment of single-cell copy-number variations Interactive analysis and quality assessment of single-cell copy-number variations Tyler Garvin, Robert Aboukhalil, Jude Kendall, Timour Baslan, Gurinder S. Atwal, James Hicks, Michael Wigler, Michael C.

More information

Nature Medicine: doi: /nm.3967

Nature Medicine: doi: /nm.3967 Supplementary Figure 1. Network clustering. (a) Clustering performance as a function of inflation factor. The grey curve shows the median weighted Silhouette widths for varying inflation factors (f [1.6,

More information

Supplementary Tables. Supplementary Figures

Supplementary Tables. Supplementary Figures Supplementary Files for Zehir, Benayed et al. Mutational Landscape of Metastatic Cancer Revealed from Prospective Clinical Sequencing of 10,000 Patients Supplementary Tables Supplementary Table 1: Sample

More information

Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA

Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA www.impactjournals.com/oncotarget/ Oncotarget, Supplementary Materials 2016 Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) DNA Supplementary Materials

More information

DNA-seq Bioinformatics Analysis: Copy Number Variation

DNA-seq Bioinformatics Analysis: Copy Number Variation DNA-seq Bioinformatics Analysis: Copy Number Variation Elodie Girard elodie.girard@curie.fr U900 institut Curie, INSERM, Mines ParisTech, PSL Research University Paris, France NGS Applications 5C HiC DNA-seq

More information

Supplementary Figures

Supplementary Figures Supplementary Figures Supplementary Figure 1. Pan-cancer analysis of global and local DNA methylation variation a) Variations in global DNA methylation are shown as measured by averaging the genome-wide

More information

underlying metastasis and recurrence in HNSCC, we analyzed two groups of patients. The

underlying metastasis and recurrence in HNSCC, we analyzed two groups of patients. The Supplementary Figures Figure S1. Patient cohorts and study design. To define and interrogate the genetic alterations underlying metastasis and recurrence in HNSCC, we analyzed two groups of patients. The

More information

HER2 FISH pharmdx TM Interpretation Guide - Breast Cancer

HER2 FISH pharmdx TM Interpretation Guide - Breast Cancer P A T H O L O G Y HER2 FISH pharmdx TM Interpretation Guide - Breast Cancer For In Vitro Diagnostic Use FDA approved as an aid in the assessment of patients for whom Herceptin TM (trastuzumab) treatment

More information

Supplementary Materials for

Supplementary Materials for www.sciencetranslationalmedicine.org/cgi/content/full/7/283/283ra54/dc1 Supplementary Materials for Clonal status of actionable driver events and the timing of mutational processes in cancer evolution

More information

Nature Genetics: doi: /ng Supplementary Figure 1. Mutational signatures in BCC compared to melanoma.

Nature Genetics: doi: /ng Supplementary Figure 1. Mutational signatures in BCC compared to melanoma. Supplementary Figure 1 Mutational signatures in BCC compared to melanoma. (a) The effect of transcription-coupled repair as a function of gene expression in BCC. Tumor type specific gene expression levels

More information

HER2 CISH pharmdx TM Kit Interpretation Guide Breast Cancer

HER2 CISH pharmdx TM Kit Interpretation Guide Breast Cancer P A T H O L O G Y HER2 CISH pharmdx TM Kit Interpretation Guide Breast Cancer FROM CERTAINTY COMES TRUST For in vitro diagnostic use HER2 CISH pharmdx Kit HER2 CISH pharmdx Kit is intended for dual-color

More information

Dako IT S ABOUT TIME. Interpretation Guide. Agilent Pathology Solutions. ALK, ROS1 and RET IQFISH probes (Dako Omnis) MET IQFISH probe (Dako Omnis)

Dako IT S ABOUT TIME. Interpretation Guide. Agilent Pathology Solutions. ALK, ROS1 and RET IQFISH probes (Dako Omnis) MET IQFISH probe (Dako Omnis) INTERPRETATION Dako Agilent Pathology Solutions IQFISH Interpretation Guide ALK, ROS1 and RET IQFISH probes (Dako Omnis) MET IQFISH probe (Dako Omnis) IT S ABOUT TIME For In Vitro Diagnostic Use ALK, ROS1,

More information

Assessment of Breast Cancer with Borderline HER2 Status Using MIP Microarray

Assessment of Breast Cancer with Borderline HER2 Status Using MIP Microarray Assessment of Breast Cancer with Borderline HER2 Status Using MIP Microarray Hui Chen, Aysegul A Sahin, Xinyan Lu, Lei Huo, Rajesh R Singh, Ronald Abraham, Shumaila Virani, Bal Mukund Mishra, Russell Broaddus,

More information

Detection of aneuploidy in a single cell using the Ion ReproSeq PGS View Kit

Detection of aneuploidy in a single cell using the Ion ReproSeq PGS View Kit APPLICATION NOTE Ion PGM System Detection of aneuploidy in a single cell using the Ion ReproSeq PGS View Kit Key findings The Ion PGM System, in concert with the Ion ReproSeq PGS View Kit and Ion Reporter

More information

Ginkgo Interactive analysis and quality assessment of single-cell CNV data

Ginkgo Interactive analysis and quality assessment of single-cell CNV data Ginkgo Interactive analysis and quality assessment of single-cell CNV data @RobAboukhalil Robert Aboukhalil, Tyler Garvin, Jude Kendall, Timour Baslan, Gurinder S. Atwal, Jim Hicks, Michael Wigler, Michael

More information

Supplemental Figure legends

Supplemental Figure legends Supplemental Figure legends Supplemental Figure S1 Frequently mutated genes. Frequently mutated genes (mutated in at least four patients) with information about mutation frequency, RNA-expression and copy-number.

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION doi: 1.138/nature8645 Physical coverage (x haploid genomes) 11 6.4 4.9 6.9 6.7 4.4 5.9 9.1 7.6 125 Neither end mapped One end mapped Chimaeras Correct Reads (million ns) 1 75 5 25 HCC1187 HCC1395 HCC1599

More information

NGS in tissue and liquid biopsy

NGS in tissue and liquid biopsy NGS in tissue and liquid biopsy Ana Vivancos, PhD Referencias So, why NGS in the clinics? 2000 Sanger Sequencing (1977-) 2016 NGS (2006-) ABIPrism (Applied Biosystems) Up to 2304 per day (96 sequences

More information

Supplementary Figure 1. Nature Neuroscience: doi: /nn.4547

Supplementary Figure 1. Nature Neuroscience: doi: /nn.4547 Supplementary Figure 1 Characterization of the Microfetti mouse model. (a) Gating strategy for 8-color flow analysis of peripheral Ly-6C + monocytes from Microfetti mice 5-7 days after TAM treatment. Living

More information

Supplementary methods:

Supplementary methods: Supplementary methods: Primers sequences used in real-time PCR analyses: β-actin F: GACCTCTATGCCAACACAGT β-actin [11] R: AGTACTTGCGCTCAGGAGGA MMP13 F: TTCTGGTCTTCTGGCACACGCTTT MMP13 R: CCAAGCTCATGGGCAGCAACAATA

More information

Advance Your Genomic Research Using Targeted Resequencing with SeqCap EZ Library

Advance Your Genomic Research Using Targeted Resequencing with SeqCap EZ Library Advance Your Genomic Research Using Targeted Resequencing with SeqCap EZ Library Marilou Wijdicks International Product Manager Research For Life Science Research Only. Not for Use in Diagnostic Procedures.

More information

Nature Genetics: doi: /ng Supplementary Figure 1. SEER data for male and female cancer incidence from

Nature Genetics: doi: /ng Supplementary Figure 1. SEER data for male and female cancer incidence from Supplementary Figure 1 SEER data for male and female cancer incidence from 1975 2013. (a,b) Incidence rates of oral cavity and pharynx cancer (a) and leukemia (b) are plotted, grouped by males (blue),

More information

Supplementary information to:

Supplementary information to: Supplementary information to: Digital Sorting of Pure Cell Populations Enables Unambiguous Genetic Analysis of Heterogeneous Formalin-Fixed Paraffin Embedded Tumors by Next Generation Sequencing Authors

More information

p.r623c p.p976l p.d2847fs p.t2671 p.d2847fs p.r2922w p.r2370h p.c1201y p.a868v p.s952* RING_C BP PHD Cbp HAT_KAT11

p.r623c p.p976l p.d2847fs p.t2671 p.d2847fs p.r2922w p.r2370h p.c1201y p.a868v p.s952* RING_C BP PHD Cbp HAT_KAT11 ARID2 p.r623c KMT2D p.v650fs p.p976l p.r2922w p.l1212r p.d1400h DNA binding RFX DNA binding Zinc finger KMT2C p.a51s p.d372v p.c1103* p.d2847fs p.t2671 p.d2847fs p.r4586h PHD/ RING DHHC/ PHD PHD FYR N

More information

Supplementary Figure 1: Features of IGLL5 Mutations in CLL: a) Representative IGV screenshot of first

Supplementary Figure 1: Features of IGLL5 Mutations in CLL: a) Representative IGV screenshot of first Supplementary Figure 1: Features of IGLL5 Mutations in CLL: a) Representative IGV screenshot of first intron IGLL5 mutation depicting biallelic mutations. Red arrows highlight the presence of out of phase

More information

Supplementary Figure 1

Supplementary Figure 1 Count Count Supplementary Figure 1 Coverage per amplicon for error-corrected sequencing experiments. Errorcorrected consensus sequence (ECCS) coverage was calculated for each of the 568 amplicons in the

More information

CONTRACTING ORGANIZATION: The Chancellor, Masters and Scholars of the University of Cambridge, Clara East, The Old Schools, Cambridge CB2 1TN

CONTRACTING ORGANIZATION: The Chancellor, Masters and Scholars of the University of Cambridge, Clara East, The Old Schools, Cambridge CB2 1TN AWARD NUMBER: W81XWH-14-1-0110 TITLE: A Molecular Framework for Understanding DCIS PRINCIPAL INVESTIGATOR: Gregory Hannon CONTRACTING ORGANIZATION: The Chancellor, Masters and Scholars of the University

More information

AP VP DLP H&E. p-akt DLP

AP VP DLP H&E. p-akt DLP A B AP VP DLP H&E AP AP VP DLP p-akt wild-type prostate PTEN-null prostate Supplementary Fig. 1. Targeted deletion of PTEN in prostate epithelium resulted in HG-PIN in all three lobes. (A) The anatomy

More information

Nature Genetics: doi: /ng.2995

Nature Genetics: doi: /ng.2995 Supplementary Figure 1 Kaplan-Meier survival curves of patients with brainstem tumors. (a) Comparison of patients with PPM1D mutation versus wild-type PPM1D. (b) Comparison of patients with PPM1D mutation

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION DOI:.38/ncb3399 a b c d FSP DAPI 5mm mm 5mm 5mm e Correspond to melanoma in-situ Figure a DCT FSP- f MITF mm mm MlanaA melanoma in-situ DCT 5mm FSP- mm mm mm mm mm g melanoma in-situ MITF MlanaA mm mm

More information

Layered-IHC (L-IHC): A novel and robust approach to multiplexed immunohistochemistry So many markers and so little tissue

Layered-IHC (L-IHC): A novel and robust approach to multiplexed immunohistochemistry So many markers and so little tissue Page 1 The need for multiplex detection of tissue biomarkers. There is a constant and growing demand for increased biomarker analysis in human tissue specimens. Analysis of tissue biomarkers is key to

More information

A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data

A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data Li and Li Genome Biology 2014, 15:473 METHOD A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data Bo Li 1 and Jun Z Li 2 Open Access Abstract Intra-tumor heterogeneity

More information

Research Strategy: 1. Background and Significance

Research Strategy: 1. Background and Significance Research Strategy: 1. Background and Significance 1.1. Heterogeneity is a common feature of cancer. A better understanding of this heterogeneity may present therapeutic opportunities: Intratumor heterogeneity

More information

Online Appendix Material and Methods: Pancreatic RNA isolation and quantitative real-time (q)rt-pcr. Mice were fasted overnight and killed 1 hour (h)

Online Appendix Material and Methods: Pancreatic RNA isolation and quantitative real-time (q)rt-pcr. Mice were fasted overnight and killed 1 hour (h) Online Appendix Material and Methods: Pancreatic RNA isolation and quantitative real-time (q)rt-pcr. Mice were fasted overnight and killed 1 hour (h) after feeding. A small slice (~5-1 mm 3 ) was taken

More information

Supplementary Online Content

Supplementary Online Content Supplementary Online Content Fumagalli D, Venet D, Ignatiadis M, et al. RNA Sequencing to predict response to neoadjuvant anti-her2 therapy: a secondary analysis of the NeoALTTO randomized clinical trial.

More information

202002, India Author affiliations

202002, India Author affiliations Copy number variation and microdeletions of the Y chromosome linked genes and loci across different categories of Indian infertile males Anju Kumari 1, Sandeep Kumar Yadav 1, M.M. Misro 2, Jamal Ahmad

More information

Frequency(%) KRAS G12 KRAS G13 KRAS A146 KRAS Q61 KRAS K117N PIK3CA H1047 PIK3CA E545 PIK3CA E542K PIK3CA Q546. EGFR exon19 NFS-indel EGFR L858R

Frequency(%) KRAS G12 KRAS G13 KRAS A146 KRAS Q61 KRAS K117N PIK3CA H1047 PIK3CA E545 PIK3CA E542K PIK3CA Q546. EGFR exon19 NFS-indel EGFR L858R Frequency(%) 1 a b ALK FS-indel ALK R1Q HRAS Q61R HRAS G13R IDH R17K IDH R14Q MET exon14 SS-indel KIT D8Y KIT L76P KIT exon11 NFS-indel SMAD4 R361 IDH1 R13 CTNNB1 S37 CTNNB1 S4 AKT1 E17K ERBB D769H ERBB

More information

Identification of Novel Variant of EML4-ALK Fusion Gene in NSCLC: Potential Benefits of the RT-PCR Method

Identification of Novel Variant of EML4-ALK Fusion Gene in NSCLC: Potential Benefits of the RT-PCR Method International journal of Biomedical science ORIGINAL ARTICLE Identification of Novel Variant of EML4-ALK Fusion Gene in NSCLC: Potential Benefits of the RT-PCR Method Martin K. H. Maus 1, 2, Craig Stephens

More information

Genomic Medicine: What every pathologist needs to know

Genomic Medicine: What every pathologist needs to know Genomic Medicine: What every pathologist needs to know Stephen P. Ethier, Ph.D. Professor, Department of Pathology and Laboratory Medicine, MUSC Director, MUSC Center for Genomic Medicine Genomics and

More information

CONTRACTING ORGANIZATION: The Chancellor, Masters and Scholars of the University of Cambridge, Clara East, The Old Schools, Cambridge CB2 1TN

CONTRACTING ORGANIZATION: The Chancellor, Masters and Scholars of the University of Cambridge, Clara East, The Old Schools, Cambridge CB2 1TN AWARD NUMBER: W81XWH-14-1-0110 TITLE: A Molecular Framework for Understanding DCIS PRINCIPAL INVESTIGATOR: Gregory Hannon CONTRACTING ORGANIZATION: The Chancellor, Masters and Scholars of the University

More information

TITLE: Identification of Chromosomes Alterations in Primary Breast Cancer Using Premature Chromosome Condensation

TITLE: Identification of Chromosomes Alterations in Primary Breast Cancer Using Premature Chromosome Condensation AD Award Number: DAMD17-99-1-9237 TITLE: Identification of Chromosomes Alterations in Primary Breast Cancer Using Premature Chromosome Condensation PRINCIPAL INVESTIGATOR: Constance A. Griffin, M.D. CONTRACTING

More information

Relationship between genomic features and distributions of RS1 and RS3 rearrangements in breast cancer genomes.

Relationship between genomic features and distributions of RS1 and RS3 rearrangements in breast cancer genomes. Supplementary Figure 1 Relationship between genomic features and distributions of RS1 and RS3 rearrangements in breast cancer genomes. (a,b) Values of coefficients associated with genomic features, separately

More information

Nature Methods: doi: /nmeth.3115

Nature Methods: doi: /nmeth.3115 Supplementary Figure 1 Analysis of DNA methylation in a cancer cohort based on Infinium 450K data. RnBeads was used to rediscover a clinically distinct subgroup of glioblastoma patients characterized by

More information

Nature Neuroscience: doi: /nn Supplementary Figure 1. MADM labeling of thalamic clones.

Nature Neuroscience: doi: /nn Supplementary Figure 1. MADM labeling of thalamic clones. Supplementary Figure 1 MADM labeling of thalamic clones. (a) Confocal images of an E12 Nestin-CreERT2;Ai9-tdTomato brain treated with TM at E10 and stained for BLBP (green), a radial glial progenitor-specific

More information

OncoPPi Portal A Cancer Protein Interaction Network to Inform Therapeutic Strategies

OncoPPi Portal A Cancer Protein Interaction Network to Inform Therapeutic Strategies OncoPPi Portal A Cancer Protein Interaction Network to Inform Therapeutic Strategies 2017 Contents Datasets... 2 Protein-protein interaction dataset... 2 Set of known PPIs... 3 Domain-domain interactions...

More information

Genetic alterations of histone lysine methyltransferases and their significance in breast cancer

Genetic alterations of histone lysine methyltransferases and their significance in breast cancer Genetic alterations of histone lysine methyltransferases and their significance in breast cancer Supplementary Materials and Methods Phylogenetic tree of the HMT superfamily The phylogeny outlined in the

More information

Fluxion Biosciences and Swift Biosciences Somatic variant detection from liquid biopsy samples using targeted NGS

Fluxion Biosciences and Swift Biosciences Somatic variant detection from liquid biopsy samples using targeted NGS APPLICATION NOTE Fluxion Biosciences and Swift Biosciences OVERVIEW This application note describes a robust method for detecting somatic mutations from liquid biopsy samples by combining circulating tumor

More information

Integrated Analysis of Copy Number and Gene Expression

Integrated Analysis of Copy Number and Gene Expression Integrated Analysis of Copy Number and Gene Expression Nexus Copy Number provides user-friendly interface and functionalities to integrate copy number analysis with gene expression results for the purpose

More information

Mosaic loss of chromosome Y in peripheral blood is associated with shorter survival and higher risk of cancer

Mosaic loss of chromosome Y in peripheral blood is associated with shorter survival and higher risk of cancer Supplementary Information Mosaic loss of chromosome Y in peripheral blood is associated with shorter survival and higher risk of cancer Lars A. Forsberg, Chiara Rasi, Niklas Malmqvist, Hanna Davies, Saichand

More information

Cytogenetics 101: Clinical Research and Molecular Genetic Technologies

Cytogenetics 101: Clinical Research and Molecular Genetic Technologies Cytogenetics 101: Clinical Research and Molecular Genetic Technologies Topics for Today s Presentation 1 Classical vs Molecular Cytogenetics 2 What acgh? 3 What is FISH? 4 What is NGS? 5 How can these

More information

5 th July 2016 ACGS Dr Michelle Wood Laboratory Genetics, Cardiff

5 th July 2016 ACGS Dr Michelle Wood Laboratory Genetics, Cardiff 5 th July 2016 ACGS Dr Michelle Wood Laboratory Genetics, Cardiff National molecular screening of patients with lung cancer for a national trial of multiple novel agents. 2000 NSCLC patients/year (late

More information

Supplementary Figures

Supplementary Figures Supplementary Figures Supplementary Figure 1 Characterization of stable expression of GlucB and sshbira in the CT26 cell line (a) Live cell imaging of stable CT26 cells expressing green fluorescent protein

More information

No evidence of clonally selected somatic genomic alterations in cancer associated

No evidence of clonally selected somatic genomic alterations in cancer associated Supplementary Data Resource No evidence of clonally selected somatic genomic alterations in cancer associated fibroblasts from human breast and ovarian carcinomas Wen Qiu, Min Hu, Anita Sridhar, Ken Opeskin,

More information

Chapter 4 Cellular Oncogenes ~ 4.6 -

Chapter 4 Cellular Oncogenes ~ 4.6 - Chapter 4 Cellular Oncogenes - 4.2 ~ 4.6 - Many retroviruses carrying oncogenes have been found in chickens and mice However, attempts undertaken during the 1970s to isolate viruses from most types of

More information

Supplementary Figures

Supplementary Figures Supplementary Figures Supplementary Figure 1. Heatmap of GO terms for differentially expressed genes. The terms were hierarchically clustered using the GO term enrichment beta. Darker red, higher positive

More information

IT S ABOUT TIME. IQFISH pharmdx Interpretation Guide THREEHOURSTHIRTYMINUTES. HER2 IQFISH pharmdxtm. TOP2A IQFISH pharmdxtm

IT S ABOUT TIME. IQFISH pharmdx Interpretation Guide THREEHOURSTHIRTYMINUTES. HER2 IQFISH pharmdxtm. TOP2A IQFISH pharmdxtm I N T E R P R E TAT I O N IQFISH pharmdx Interpretation Guide TM HER2 IQFISH pharmdxtm TOP2A IQFISH pharmdxtm Breast carcinoma (FFPE) stained with HER2 IQFISH pharmdx Breast carcinoma (FFPE) stained with

More information

Figure S2. Distribution of acgh probes on all ten chromosomes of the RIL M0022

Figure S2. Distribution of acgh probes on all ten chromosomes of the RIL M0022 96 APPENDIX B. Supporting Information for chapter 4 "changes in genome content generated via segregation of non-allelic homologs" Figure S1. Potential de novo CNV probes and sizes of apparently de novo

More information

Accel-Amplicon Panels

Accel-Amplicon Panels Accel-Amplicon Panels Amplicon sequencing has emerged as a reliable, cost-effective method for ultra-deep targeted sequencing. This highly adaptable approach is especially applicable for in-depth interrogation

More information

Supplementary Figures

Supplementary Figures Supplementary Figures Supplementary Figure 1. Confirmation of Dnmt1 conditional knockout out mice. a, Representative images of sorted stem (Lin - CD49f high CD24 + ), luminal (Lin - CD49f low CD24 + )

More information

CDH1 truncating alterations were detected in all six plasmacytoid-variant bladder tumors analyzed by whole-exome sequencing.

CDH1 truncating alterations were detected in all six plasmacytoid-variant bladder tumors analyzed by whole-exome sequencing. Supplementary Figure 1 CDH1 truncating alterations were detected in all six plasmacytoid-variant bladder tumors analyzed by whole-exome sequencing. Whole-exome sequencing of six plasmacytoid-variant bladder

More information

Supplementary Figure 1. Using DNA barcode-labeled MHC multimers to generate TCR fingerprints

Supplementary Figure 1. Using DNA barcode-labeled MHC multimers to generate TCR fingerprints Supplementary Figure 1 Using DNA barcode-labeled MHC multimers to generate TCR fingerprints (a) Schematic overview of the workflow behind a TCR fingerprint. Each peptide position of the original peptide

More information

MSI positive MSI negative

MSI positive MSI negative Pritchard et al. 2014 Supplementary Figure 1 MSI positive MSI negative Hypermutated Median: 673 Average: 659.2 Non-Hypermutated Median: 37.5 Average: 43.6 Supplementary Figure 1: Somatic Mutation Burden

More information

Utility of Adequate Core Biopsy Samples from Ultrasound Biopsies Needed for Today s Breast Pathology

Utility of Adequate Core Biopsy Samples from Ultrasound Biopsies Needed for Today s Breast Pathology Utility of Adequate Core Biopsy Samples from Ultrasound Biopsies Needed for Today s Breast Pathology Ugur Ozerdem, M.D. 1 Abstract Background: There is a paradigm shift in breast biopsy philosophy. In

More information

BWA alignment to reference transcriptome and genome. Convert transcriptome mappings back to genome space

BWA alignment to reference transcriptome and genome. Convert transcriptome mappings back to genome space Whole genome sequencing Whole exome sequencing BWA alignment to reference transcriptome and genome Convert transcriptome mappings back to genome space genomes Filter on MQ, distance, Cigar string Annotate

More information

S1 Appendix: Figs A G and Table A. b Normal Generalized Fraction 0.075

S1 Appendix: Figs A G and Table A. b Normal Generalized Fraction 0.075 Aiello & Alter (216) PLoS One vol. 11 no. 1 e164546 S1 Appendix A-1 S1 Appendix: Figs A G and Table A a Tumor Generalized Fraction b Normal Generalized Fraction.25.5.75.25.5.75 1 53 4 59 2 58 8 57 3 48

More information

Supplemental Information. 3D-CLEM Reveals that a Major Portion. of Mitotic Chromosomes Is Not Chromatin

Supplemental Information. 3D-CLEM Reveals that a Major Portion. of Mitotic Chromosomes Is Not Chromatin Molecular Cell, Volume 64 Supplemental Information 3D-CLEM Reveals that a Major Portion of Mitotic Chromosomes Is Not Chromatin Daniel G. Booth, Alison J. Beckett, Oscar Molina, Itaru Samejima, Hiroshi

More information

iplex genotyping IDH1 and IDH2 assays utilized the following primer sets (forward and reverse primers along with extension primers).

iplex genotyping IDH1 and IDH2 assays utilized the following primer sets (forward and reverse primers along with extension primers). Supplementary Materials Supplementary Methods iplex genotyping IDH1 and IDH2 assays utilized the following primer sets (forward and reverse primers along with extension primers). IDH1 R132H and R132L Forward:

More information

Clonal evolution of human cancers

Clonal evolution of human cancers Clonal evolution of human cancers -Pathology-based microdissection and genetic analysis precisely demonstrates molecular evolution of neoplastic clones- Hiroaki Fujii, MD Ageo Medical Laboratories, Yashio

More information

Supplementary Figure 1. Experimental paradigm. A combination of genome and exome sequencing coupled with array-comparative genome hybridization was

Supplementary Figure 1. Experimental paradigm. A combination of genome and exome sequencing coupled with array-comparative genome hybridization was Supplementary Figure 1. Experimental paradigm. A combination of genome and exome sequencing coupled with array-comparative genome hybridization was performed on a total of 85 SS patients. Data filtration

More information

Nature Getetics: doi: /ng.3471

Nature Getetics: doi: /ng.3471 Supplementary Figure 1 Summary of exome sequencing data. ( a ) Exome tumor normal sample sizes for bladder cancer (BLCA), breast cancer (BRCA), carcinoid (CARC), chronic lymphocytic leukemia (CLLX), colorectal

More information

The Chancellor, Masters and Scholars of the University of Cambridge, Clara East, The Old Schools, Cambridge CB2 1TN

The Chancellor, Masters and Scholars of the University of Cambridge, Clara East, The Old Schools, Cambridge CB2 1TN AWARD NUMBER: W81XWH-14-1-0110 TITLE: A Molecular Framework for Understanding DCIS PRINCIPAL INVESTIGATOR: Gregory Hannon CONTRACTING ORGANIZATION: The Chancellor, Masters and Scholars of the University

More information

Iso-Seq Method Updates and Target Enrichment Without Amplification for SMRT Sequencing

Iso-Seq Method Updates and Target Enrichment Without Amplification for SMRT Sequencing Iso-Seq Method Updates and Target Enrichment Without Amplification for SMRT Sequencing PacBio Americas User Group Meeting Sample Prep Workshop June.27.2017 Tyson Clark, Ph.D. For Research Use Only. Not

More information

MET skipping mutation, EGFR

MET skipping mutation, EGFR New NSCLC biomarkers in clinical research: detection of MET skipping mutation, EGFR T790M, and other important biomarkers Fernando López-Ríos Laboratorio de Dianas Terapéuticas Hospital Universitario HM

More information

AD (Leave blank) TITLE: Genomic Characterization of Brain Metastasis in Non-Small Cell Lung Cancer Patients

AD (Leave blank) TITLE: Genomic Characterization of Brain Metastasis in Non-Small Cell Lung Cancer Patients AD (Leave blank) Award Number: W81XWH-12-1-0444 TITLE: Genomic Characterization of Brain Metastasis in Non-Small Cell Lung Cancer Patients PRINCIPAL INVESTIGATOR: Mark A. Watson, MD PhD CONTRACTING ORGANIZATION:

More information

Supplementary Figure 1: Tissue of Origin analysis on 152 cell lines. (a) Heatmap representation of the 30 Tissue scores for the 152 cell lines.

Supplementary Figure 1: Tissue of Origin analysis on 152 cell lines. (a) Heatmap representation of the 30 Tissue scores for the 152 cell lines. Supplementary Figure 1: Tissue of Origin analysis on 152 cell lines. (a) Heatmap representation of the 30 Tissue scores for the 152 cell lines. The scores summarize the global expression of the tissue

More information

Supplemental Figure S1. Expression of Cirbp mrna in mouse tissues and NIH3T3 cells.

Supplemental Figure S1. Expression of Cirbp mrna in mouse tissues and NIH3T3 cells. SUPPLEMENTAL FIGURE AND TABLE LEGENDS Supplemental Figure S1. Expression of Cirbp mrna in mouse tissues and NIH3T3 cells. A) Cirbp mrna expression levels in various mouse tissues collected around the clock

More information

Investigating Breast Cancer Evolution with Single Cell Genomics

Investigating Breast Cancer Evolution with Single Cell Genomics Investigating Breast Cancer Evolution with Single Cell Genomics AACR Drug Sensitivity & Resistance June 21 st, 2014 Nicholas E. Navin MD Anderson Cancer Center Innovation in Breast Cancer Madrid, Spain

More information

Supplementary Information. Supplementary Figures

Supplementary Information. Supplementary Figures Supplementary Information Supplementary Figures.8 57 essential gene density 2 1.5 LTR insert frequency diversity DEL.5 DUP.5 INV.5 TRA 1 2 3 4 5 1 2 3 4 1 2 Supplementary Figure 1. Locations and minor

More information

Supplementary Figure 1 Transcription assay of nine ABA-responsive PP2C. Transcription assay of nine ABA-responsive PP2C genes. Total RNA was isolated

Supplementary Figure 1 Transcription assay of nine ABA-responsive PP2C. Transcription assay of nine ABA-responsive PP2C genes. Total RNA was isolated Supplementary Figure 1 Transcription assay of nine ABA-responsive PP2C genes. Transcription assay of nine ABA-responsive PP2C genes. Total RNA was isolated from 7 day-old seedlings treated with or without

More information

(a) Schematic diagram of the FS mutation of UVRAG in exon 8 containing the highly instable

(a) Schematic diagram of the FS mutation of UVRAG in exon 8 containing the highly instable Supplementary Figure 1. Frameshift (FS) mutation in UVRAG. (a) Schematic diagram of the FS mutation of UVRAG in exon 8 containing the highly instable A 10 DNA repeat, generating a premature stop codon

More information

Mutation Detection and CNV Analysis for Illumina Sequencing data from HaloPlex Target Enrichment Panels using NextGENe Software for Clinical Research

Mutation Detection and CNV Analysis for Illumina Sequencing data from HaloPlex Target Enrichment Panels using NextGENe Software for Clinical Research Mutation Detection and CNV Analysis for Illumina Sequencing data from HaloPlex Target Enrichment Panels using NextGENe Software for Clinical Research Application Note Authors John McGuigan, Megan Manion,

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION doi:10.1038/nature10866 a b 1 2 3 4 5 6 7 Match No Match 1 2 3 4 5 6 7 Turcan et al. Supplementary Fig.1 Concepts mapping H3K27 targets in EF CBX8 targets in EF H3K27 targets in ES SUZ12 targets in ES

More information

Molecular Testing in Lung Cancer

Molecular Testing in Lung Cancer Molecular Testing in Lung Cancer Pimpin Incharoen, M.D. Assistant Professor, Thoracic Pathology Department of Pathology, Ramathibodi Hospital Genetic alterations in lung cancer Source: Khono et al, Trans

More information

Whole Genome and Transcriptome Analysis of Anaplastic Meningioma. Patrick Tarpey Cancer Genome Project Wellcome Trust Sanger Institute

Whole Genome and Transcriptome Analysis of Anaplastic Meningioma. Patrick Tarpey Cancer Genome Project Wellcome Trust Sanger Institute Whole Genome and Transcriptome Analysis of Anaplastic Meningioma Patrick Tarpey Cancer Genome Project Wellcome Trust Sanger Institute Outline Anaplastic meningioma compared to other cancers Whole genomes

More information

Expanded View Figures

Expanded View Figures Molecular Systems iology Tumor CNs reflect metabolic selection Nicholas Graham et al Expanded View Figures Human primary tumors CN CN characterization by unsupervised PC Human Signature Human Signature

More information

Supplementary Figure 1. Estimation of tumour content

Supplementary Figure 1. Estimation of tumour content Supplementary Figure 1. Estimation of tumour content a, Approach used to estimate the tumour content in S13T1/T2, S6T1/T2, S3T1/T2 and S12T1/T2. Tissue and tumour areas were evaluated by two independent

More information

Characterisation of structural variation in breast. cancer genomes using paired-end sequencing on. the Illumina Genome Analyser

Characterisation of structural variation in breast. cancer genomes using paired-end sequencing on. the Illumina Genome Analyser Characterisation of structural variation in breast cancer genomes using paired-end sequencing on the Illumina Genome Analyser Phil Stephens Cancer Genome Project Why is it important to study cancer? Why

More information

Supplementary Figure S1. Gene expression analysis of epidermal marker genes and TP63.

Supplementary Figure S1. Gene expression analysis of epidermal marker genes and TP63. Supplementary Figure Legends Supplementary Figure S1. Gene expression analysis of epidermal marker genes and TP63. A. Screenshot of the UCSC genome browser from normalized RNAPII and RNA-seq ChIP-seq data

More information

Qué hemos aprendido hasta hoy? What have we learned so far?

Qué hemos aprendido hasta hoy? What have we learned so far? Qué hemos aprendido hasta hoy? What have we learned so far? Luís Costa Hospital de Santa Maria & Instituto de Medicina Molecular Faculdade de Medicina de Lisboa Disclosures Research Grants: Amgen; Novartis;

More information

A complete next-generation sequencing workfl ow for circulating cell-free DNA isolation and analysis

A complete next-generation sequencing workfl ow for circulating cell-free DNA isolation and analysis APPLICATION NOTE Cell-Free DNA Isolation Kit A complete next-generation sequencing workfl ow for circulating cell-free DNA isolation and analysis Abstract Circulating cell-free DNA (cfdna) has been shown

More information

Nature Genetics: doi: /ng Supplementary Figure 1. Somatic coding mutations identified by WES/WGS for 83 ATL cases.

Nature Genetics: doi: /ng Supplementary Figure 1. Somatic coding mutations identified by WES/WGS for 83 ATL cases. Supplementary Figure 1 Somatic coding mutations identified by WES/WGS for 83 ATL cases. (a) The percentage of targeted bases covered by at least 2, 10, 20 and 30 sequencing reads (top) and average read

More information

Figure S4. 15 Mets Whole Exome. 5 Primary Tumors Cancer Panel and WES. Next Generation Sequencing

Figure S4. 15 Mets Whole Exome. 5 Primary Tumors Cancer Panel and WES. Next Generation Sequencing Figure S4 Next Generation Sequencing 15 Mets Whole Exome 5 Primary Tumors Cancer Panel and WES Get coverage of all variant loci for all three Mets Variant Filtering Sequence Alignments Index and align

More information

Supplemental Figure S1A Notch1

Supplemental Figure S1A Notch1 Supplemental Figure S1A Notch1 erage) epth of Cove ormalized De Log1(No Notch exons Figure S1: A) Relative coverage of Notch1 and Notch 2 exons in HCC2218, HCC1187, MB157, MDA-MB157 cell lines. Blue color

More information

File name: Supplementary Information Description: Supplementary Figures, Supplementary Table and Supplementary References

File name: Supplementary Information Description: Supplementary Figures, Supplementary Table and Supplementary References File name: Supplementary Information Description: Supplementary Figures, Supplementary Table and Supplementary References File name: Supplementary Data 1 Description: Summary datasheets showing the spatial

More information

FONS Nové sekvenační technologie vklinickédiagnostice?

FONS Nové sekvenační technologie vklinickédiagnostice? FONS 2010 Nové sekvenační technologie vklinickédiagnostice? Sekvenování amplikonů Sequence capture Celogenomové sekvenování FONS 2010 Sekvenování amplikonů Amplicon sequencing - amplicon sequencing enables

More information

Expanded View Figures

Expanded View Figures EMO Molecular Medicine Proteomic map of squamous cell carcinomas Hanibal ohnenberger et al Expanded View Figures Figure EV1. Technical reproducibility. Pearson s correlation analysis of normalised SILC

More information

Supplementary Materials for

Supplementary Materials for www.sciencetranslationalmedicine.org/cgi/content/full/4/117/117ra8/dc1 Supplementary Materials for Notch4 Normalization Reduces Blood Vessel Size in Arteriovenous Malformations Patrick A. Murphy, Tyson

More information

Supplementary Figure 1. Schematic diagram of o2n-seq. Double-stranded DNA was sheared, end-repaired, and underwent A-tailing by standard protocols.

Supplementary Figure 1. Schematic diagram of o2n-seq. Double-stranded DNA was sheared, end-repaired, and underwent A-tailing by standard protocols. Supplementary Figure 1. Schematic diagram of o2n-seq. Double-stranded DNA was sheared, end-repaired, and underwent A-tailing by standard protocols. A-tailed DNA was ligated to T-tailed dutp adapters, circularized

More information