Dec. 7, 2017. Rogan PK, Mucaki EJ. Comment on PMID 29185120: Characterization of a novel germline BRCA1 splice variant, c.5332+4delA. In: PubMed Commons [Internet]. Bethesda (MD): National Library of Medicine; 2017 Nov 28 [cited 2017 Dec 7].

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Peter Rogan2017 Dec 07 5:24 p.m.

We have analyzed this mutation with the Automated Splice Site and Exon Definition Analysis server (ASSEDA). The 1 nt deletion in the splice donor of exon 20 reduces the strength of this site from 11.5 -> 4.1 bits. (100/[27.4 bits] = 0.6% binding affinity)

The information theory-based approach used in ASSEDA predicts isoform abundance and computes the fold changes in binding affinity from mutations (Mucaki EJ, 2013), which corresponds to the degree of exon skipping in this case. The reduction in splice site strength is much greater than the estimates given by the ad hoc methods used in the paper. LOH was not complete; some of the observed expression may have been derived from the contaminating normal allele. In fact, had the loss of function in splice site recognition only been 25-40% according to the paper, it could have been classified as a variant of unknown significance, or possibly as benign (as we suggested in Mucaki EJ, 2011).

Dec 12, 2017. Comment on PubMed PMID 23169495: Analysis of the effects of rare variants on splicing identifies alterations in GABAA receptor genes in autism spectrum disorder individuals.

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Rogan PK, Mucaki EJ. Comment on PMID 23169495: Analysis of the effects of rare variants on splicing identifies alterations in GABAA receptor genes in autism spectrum disorder individuals. In: PubMed Commons [Internet]. Bethesda (MD): National Library of Medicine; 2012 Nov 21 [cited 2017 Dec 12].

Peter Rogan2017 Dec 12 09:53 a.m

Regarding GABRQ:c.306G>C: Whereas none of the splicing analysis programs tested predict outcomes shown in the mini-gene construct shown in Figure 2A, information theory-based exon definition analyses using ASSEDA (Mucaki EJ, 2013) was completely concordant. A novel band 116nt longer than the product expected from the wild type exon is observed. The mutation reduces the strength of the natural donor splice site of exon 3 from 9.5 -> 4.5 bits (32 fold). The pre-existing intronic cryptic site 116 nt downstream (8.6 bits) is 17 fold stronger than the mutated splice site. ASSEDA indicates that the total exon information (Ri,total) of wildtype exon is reduced (19.8 -> 14.8 bits) and the corresponding strength of the gap-surprisal adjusted cryptic exon significantly exceeds this (17.7 bits). The wildtype exon is predicted to be ~5-6 fold more abundant than the cryptic exon BEFORE mutation, and the cryptic exon is predicted to be ~8 fold more abundant AFTER mutation.

Jan. 13 and 21, 2018. Comments on PubMed PMID 29280214: Thorough in silico and in vitro cDNA analysis of 21 putative BRCA1 and BRCA2 splice variants and a complex tandem duplication in BRCA2, allowing the identification of activated cryptic splice donor sites in BRCA2 exon 11.

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We have posted a comment in PubMed Commons about Baert et al. “Thorough in silico and in vitro cDNA analysis of 21 putative BRCA1 and BRCA2 splice variants and a complex tandem duplication in BRCA2, allowing the identification of activated cryptic splice donor sites in BRCA2 exon 11.” (2017) (doi: 10.1002/humu.23390). The updated comments can be found at: https://www.ncbi.nlm.nih.gov/pubmed/29280214#comments. They have been highlighted twice by PubMed Commons as a “Top Comment”.

NB: We have exchanged views with Dr. Claes (senior author), who has inquired about our NGS pipeline for splicing mutation analysis, MutationForecaster (www.mutationforecaster.com):

Peter Rogan2018 Jan 12 2:39 p.m.edited 2 of 2 people found this helpful

Twenty one BRCA1 and BRCA2 mRNA splice site variants were analyzed by semi-quantitative RT-PCR, with commercial software that scores putative splice sites by ad hoc methods, and with bioinformatic models based on Adaboost and Random Forest, which are general machine learning approaches. The authors cited our review on interpretation of splicing mutations (Caminsky N, 2014), however the analytic approach described in that paper was not evaluated. As an update to our previous BRCA mutation study (Mucaki EJ, 2011), we carried out information theory-based splicing analysis of all potential splicing mutations listed in Supplemental Table S3. The splicing consequences of all variants were accurately predicted by information analysis. We also report results of exon definition-based mRNA splicing mutation analysis (Mucaki EJ, 2013), which infers relative abundance of wild type and mutated splice isoforms from total splicing information content of each prospective exon. Due to length limitations in PubMed Commons commenting system, detailed results for each variant are described in: https://doi.org/10.5281/zenodo.1146708

Also, during our analysis, some inconsistencies in mutation designation or interpretation were noted in the paper: (1) The complex BRCA2duplication described in this article (c.425+415_4780dup[insGATCGCAGTGA]) is sometimes referred to as “c.426-415_4780dup[insGATCGCAGTGA]” (e.g. the title of Figure 5, and Suppl. Table S3), which are not congruent mutations. The true mutation is likely the former, as the Figure 5 legend describes an mRNA splice form that includes 293nt of intron 4. If the duplication was c.426-415_4780dup[insGATCGCAGTGA], the intron inclusion would only be 205nt long. (2) We report an additional inconsistency in regards to Figure 5: The legend of Figure 5E describes a splice form where a truncated exon 11 junctions with the aforementioned 11nt insertion. However, the diagram and the electropherogram in Figure 5e shows exon 11 (ending at c.2398) sharing a junction with the beginning of exon 5. The latter is most likely the correct isoform, as an acceptor is not predicted at the junction between c.4780 and the 11nt insertion.

  • Kathleen B M Claes2018 Jan 17 10:44 a.m. 2 of 2 people found this helpful

    Dear dr Rogan, thank you very much for your constructive comments. It is very interesting to learn that your exon definition-based mRNA splicing analyses are in agreement with our cDNA analyses for all variants we studied (an overview is provided in Suppl Table S1 of our paper – not S3). I read the detailed comments on the URL you referred to. How easy can this approach be implemented in an NGS data analysis pipeline? Can you define cut-offs in this program to indicate when cDNA analysis is warranted?

    I also would like to thank you for alerting us about the typing error for the Multi-exon duplication in BRCA2 – the correct nomenclature for this duplication is indeed c.426+415_4780dup{insGATCGCAGTGA}. We corrected this in the final proofs.

    • Peter Rogan2018 Jan 21 1:20 p.m.edited 1 of 1 people found this helpful

      The results reported in Table S1 of the different bioinformatic methods were difficult for us to assess. For example, why were there no bioinformatic analyses for c.426+415_4780dup(insGATCGCAGTGA)? Our analysis includes this mutation. Model cutoffs for these bioinformatic methods are defined arbitrarily because they are based on underlying datasets with unpublished or unknown content; furthermore, the binding site models are not easily reproduced, in part because they are not actually based on binding site affinities (Rogan PK, 2013).

      The details of the methods and source data we use to derive our information weight matrices and the matrices themselves are available (Rogan PK, 2003). The information contents of splice recognition sites or exons are expressed in units of bits, which have been formally proven to be related to binding site affinity through the second law of thermodynamics (Schneider TD, 1997, Rogan PK, 1998). In fact, relative entropy used by maxEntscan, violates the triangle inequality which is a fundamental requirement of the second law (Schneider TD, 1999). These articles demonstrate the cutoff for true binding sites is very close to the theoretical minimum of zero bits (Delta G = 0). We have also demonstrated this thermodynamic threshold holds for other types of binding sites (Lu R, 2017).

      Our pipeline for NGS data analysis has been validated extensively (Shirley BC, 2013, Viner C, 2014, Dorman SN, 2014, Caminsky NG, 2016, Mucaki EJ, 2016, Yang XR, 2017, Dos Santos ES, 2017). The URL of the MutationForecaster pipeline is given in the document linked to our previous PubMed Commons post .

 

PubMedCommonsentry1-12-2018

 

 

December 12, 2017. New preprint predicting response to platin drugs

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Mucaki et al. Predicting Response to Platin Chemotherapy Agents with Biochemically-inspired Machine Learning. bioRxiv.

https://doi.org/10.1101/231712

Abstract

Selection of effective drugs that accurately predict chemotherapy response could improve cancer outcomes. We derive optimized gene signatures for response to common platinum-based drugs, cisplatin, carboplatin, and oxaliplatin, and respectively validate each with bladder, ovarian, and colon cancer patient data. Initially, using breast cancer cell line gene expression and growth inhibition (GI50) data, we performed backwards feature selection with cross-validation to derive predictive gene sets in a supervised support vector machine (SVM) learning approach. These signatures were also verified in bladder cancer cell lines. Aside from published associations between drugs and genes, we also expanded these gene signatures using a systems biology approach. Signatures at different GI50 thresholds distinguishing sensitivity from resistance to each drug contrast the contributions of different genes at extreme vs. median thresholds. An ensemble machine learning technique combining different GI50 thresholds was used to create threshold independent gene signatures. The most accurate models for each platinum drug in cell lines consisted of cisplatin: BARD1, BCL2, BCL2L1, CDKN2C, FAAP24, FEN1, MAP3K1, MAPK13, MAPK3, NFKB1, NFKB2, SLC22A5, SLC31A2, TLR4, TWIST1; carboplatin: AKT1, EIF3K, ERCC1, GNGT1, GSR, MTHFR, NEDD4L, NLRP1, NRAS, RAF1, SGK1, TIGD1, TP53, VEGFB, VEGFC; and oxaliplatin: BRAF, FCGR2A, IGF1, MSH2, NAGK, NFE2L2, NQO1, PANK3, SLC47A1, SLCO1B1, UGT1A1. Recurrence in bladder urothelial carcinoma patients from the Cancer Genome Atlas (TCGA) treated with cisplatin after 18 months was 71% accurate (59% in disease-free patients). In carboplatin-treated ovarian cancer patients, predicted recurrence was 60.2% (61% disease-free) accurate after 4 years, while the oxaliplatin signature predicted disease-free colorectal cancer patients with 72% accuracy (54.5% for recurrence) after 1 year. The best performing cisplatin model best predicted outcome for non-smoking TCGA bladder cancer patients (100% accuracy for recurrent, 57% for disease-free; N=19), the median GI50 model (GI50 = 5.12) predicted outcome in smokers with 79% with recurrence, and 62% who were disease free; N=35). Cisplatin and carboplatin signatures were comprised of overlapping gene sets and GI50 values, which contrasted with models for oxaliplatin response.

December 1, 2017. New bespoke variant interpretation service

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MutationForecaster® is now available as a custom analysis service that we provide to you on your data. We’ve listened to you, let us assume the task of performing information theory-based analysis for you. We now offer a Bespoke service that allows you to get fully documented reports based on analysis of variants that you submit to us. Please click on the Learn More link below for more information. Our tools for non-coding variant interpretation utilize an information theory-based approach only available through CytoGnomix. No other service provides the patented, molecular diagnostic information that MutationForecaster® generates.

MutationForecaster1pg

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

November 20, 2017. New publication on inherited breast and ovarian cancer accepted for publication

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Collaboration with a French consortium to study non-coding variants in BRCA1 and BRCA2 in patients with a family history of breast and ovarian cancer:

Santana dos Santos, E, Caputo, S.M., Castera, L, Gendrot, M, Briaux, A., Breault, M, Krieger, S, Rogan, P.K, Mucaki, E.J., Bieche, I, Houdayer, C, Vaur, D, Stoppa-Lyonnet, D, Brown, M, Lallemand, F., Rouleau, E. Assessment of functional impact of germline BRCA1/2 variants located in noncoding regions in families with breast and or ovarian cancer predisposition, Breast Cancer Research and Treatment, in press.

c130BRCA1

November 11, 2017. ADCI software evaluation

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The International Atomic Energy Agency (IAEA), within the recently initiated Coordinated Research Project: “Applications of Biological Dosimetry Methods in Radiation Oncology, Nuclear Medicine, Diagnostic and Interventional Radiology” (E35010) will develop clinical applications for biodosimetric techniques, in particular the dicentric assay. Many of the coordinating groups have developed the dicentric assay in their labs, but generally results are interpreted manually.

Clinical applications of biodosimetric techniques will only be routinely applied if less manpower-intensive techniques are employed. The Cytognomix ADCI software system addresses this critical need.

At the first meeting of the Research Coordinators of E35010, all respondents elected to receive evaluation versions of this software:

CRP Graphical Survey Results

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

October 30, 2017. CytoGnomix signs agreement with International Atomic Energy Agency

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Cytognomix logo

NEWS RELEASE

For immediate release

Ontario company contributes to radiation biodosimetry project at the International Atomic Energy Agency

Cytognomix accelerates estimation of radiation exposure by participating institutions of International Atomic Energy Agency (IAEA) Member States

October 30, 2017                                London, Ontario, Canada                              Cytognomix Inc

Calibration of radiation exposure needs to be accurate for effective cancer treatment. Treatment of radiation overexposures depends on precise measurement of absorbed dose and the type of radiation received. Quantification of radiation exposure by biodosimetry testing needs to be timely for patients to benefit.

The IAEA is committed to encouraging and assisting research on, and development of practical applications of atomic energy for peaceful uses throughout the world. It has extended the opportunity to research institutes in Member States to participate in the Coordinated Research Project (CRP) E35010 entitled ‘Applications of Biological Dosimetry Methods in Radiation Oncology, Nuclear Medicine, and Diagnostic and Interventional Radiology.’

The IAEA is sponsoring CytoGnomix’s Research Project, entitled ‘Determination of Radiation Exposure by Fully Automated Dicentric Chromosome Analysis.’  This project will enable laboratories and research institutions of Member States to use Cytognomix’s technology to accelerate testing radiation exposure.

In this project, Cytognomix Inc. will use its systems to automatically analyze digital images of chromosomes exposed to radiation to estimate exposure. Results obtained by biodosimetry laboratories at Health Canada and Canadian Nuclear Laboratories suggest that the results are similar to traditional manual analyses, but are achieved considerably more quickly. This research will expand access to these systems by other laboratories participating in IAEA’s Coordinated Research Project.

Accuracy and speed of the automated system  will be compared with previous results from collaborating CRP laboratories that were obtained by manual or computer-assisted DCA scoring. It is  anticipated that cell image data obtained from test samples in prior or current international joint laboratory exercises or  independent assay validation activities will be reused in this study. Each collaborating laboratory will also receive a demonstration software version containing their calibration curve and test sample data. Dose estimates obtained by CytoGnomix will be  compared with results obtained by collaborators. If the previous results are comparable to those obtained with ADCI in  different laboratories, this will establish the feasibility of undertaking larger scale, batch analysis of populations of individuals that  have potentially received radiation exposure.  A unique aspect of the proposed study will assess whether it enables greater standardization of results obtained by  different laboratories, because all labs will use a common algorithm to process their data, while still allowing different labs to  customize their own calibration curves for determining unknown radiation exposures, which addresses differences in chromosome preparation methods and radiation calibration sources between labs.

Quotes

“The IAEA has recognized the critical need for faster approaches to accurately determine radiation exposure that address impending needs by its members. By sponsoring our project, CytoGnomix will have a unique opportunity to provide hands-on experiences to radiation biodosimetry laboratories and centres worldwide.”

Dr. Peter K. Rogan

President of Cytognomix Inc.

 

Quick facts

  • Established in 2009, CytoGnomix Inc. is a biotechnology company that designs and markets advanced genomic reagents and software-based solutions. Its products personalize the diagnosis, evaluation and management of cancer, prenatal disorders and other genetic diseases.
  • CytoGnomix’s ADCI software system selects high-quality cells from all types of digital images for analysis, identifies chromosome anomalies, builds biodosimetry calibration curves and estimates exposure in less than an hour.
  • In 2017, IAEA is sponsoring 35 Cooperative Research Activities on diverse topics concerning the peaceful use of atomic energy. CRP E35010, which is focused on the biological effects of radiation, is one of 5 projects focused on human health. The decision to award a research contract or agreement is made after careful consideration of the technical merits of the proposal, the compatibility of the project with the IAEA’s own functions and approved programmes, the availability of appropriate facilities and personnel in the institution and previous research work related to the project. Where it is recognized that the award of a particular research or technical contract or research agreement would materially assist one of the IAEA’s programmes, an invitation is sent to those institutions believed to have the necessary facilities and personnel, and the Government of the Member State concerned is kept informed.

 

Associated links

CytoGnomix: company website;  radiation biodosimetry website

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IAEA:  website

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Contacts

Corporate Communications, CytoGnomix

(1) 519-661-4255

info@cytognomix.com

 

 

 

October 4, 2017. Three upcoming presentations at the American Society of Human Genetics annual conference

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PgmNr 182: Splicing mutation risk analysis in hereditary breast and ovarian cancer exomes. (Platform)

Thurs, Oct 19. 11:00am -12:30pm. Session 40. Defining High Risk in Cancer. Room 230C – Level 2/Orlando Convention Center 

E.J. Mucaki 1; B.C. Shirley 2; S.N. Dorman 1; P.K. Rogan 1,2  1) Biochemistry, University of Western Ontario, London, Ontario, Canada; 2) CytoGnomix Inc, London, Ontario, Canada

Genetic testing of patients with inherited cancer frequently reveals variants of unknown significance (VUS). We have presented an Information Theory (IT) framework to predict and prioritize coding and non-coding VUS in hereditary breast and ovarian cancer (BRCA) patients, including effects on mRNA splicing1,2. We investigated the exome wide distribution of predicted mRNA splicing mutations in a large BRCA cohort. Predicted splicing mutations in IT-based splicing analysis of all variant data from AmbryShare BRCA exome (n=11,416; with 1.2 million VUS) and the control genome Aggregation Databases (gnomAD; n=138,632) were identified using the Shannon splicing mutation software pipeline3. IT-flagged variant frequencies (decreasing Ri values [in bits] of either leaky or inactivated natural splice sites [∆Ri >4 bits and Ri ≤ 1.6] or strengthened cryptic splices sites with an Ri exceeding that of adjacent natural sites) were compared for each gene using odds ratios (OR). ORA is defined as the ratio of frequencies of the same flagged variants in a gene in AmbryShare relative to gnomAD. ORP is based on the ratio of frequencies of all flagged variants in a gene in AmbryShare relative to all flagged variants in that gene in gnomAD. A greater number of IT-flagged variants were present in AmbryShare than in gnomAD among 2012 genes with severe splicing mutations. Increasing the ∆Ri threshold disproportionally decreases the number of flagged variants in gnomAD due to fewer severe splicing mutations. Variants that abolish natural splice sites flagged known inherited breast cancer genes with respectively increased ORA and ORP inATM (493, 407), BARD1 (407, 407), BRCA1 (19, 14), BRCA2 (54, 54),CDH1 (549, 549), MLH1 (303, 303), MUTYH (95, 11), and PALB2 (233, 116). Other flagged breast cancer-related genes with high OR includeAAMP, C1QTNF6, CDK3, FOLR1, PRLR, RAD50, RING1, S100A2, SRGN,TMSB10, TYRO3, and VIM. Notable highly mutated genes from other cancers include GKN1 (gastric), C1orf61 (hepatocellular), CREM(prostate), PNKP (multiple), PPP1CA (gastric) and ZFAND2B (myeloid). Flagged genes not known to be linked to cancer include ATP1A4, MFF,PACSIN1, PTS, and USH1C. Severe splicing mutations occur more frequently in inherited and somatic breast cancer genes as well as in other genes in BRCA populations.
1Mucaki et al. BMC Med. Genom. 9:19, 2016; 2Caminsky et al. Hum. Mut. 37:640, 2016; 3Shirley et al. Genom. Prot. Bioinf. 11:75, 2013.    Keywords: Cancer; Bioinformatics; Genomics; Population genetics; Statistical genetics

 

PgmNr 1268/T: Accurate radiation biodosimetry through automation of metaphase cell image selection and chromosome segmentation. (Poster)

Thurs, Oct 19.  2:00pm – 4:00pm. Bioinformatics and Computational Approaches. Exhibit Hall, Level 1, Orlando Convention Center 

Y. Li 1; J. Liu 2; B. Shirley 1; R. Wilkins 3; F. Flegal 4; J.H.M. Knoll 1,2; P.K. Rogan 1,2   1) CytoGnomix Inc, London, Ontario, Canada; 2) University of Western Ontario, London, Ontario Canada; 3) Health Canada, Ottawa, Ontario, Canada; 4) Canadian Nuclear Laboratories, Chalk River, Ontario, Canada

The dicentric chromosome (DC) assay is a standardized method that is recommended for determination of biologic radiation exposure1,2. Software to fully automate this assay has been developed in our laboratory3. This method relies on high quality microscope-derived images of metaphase cells to reduce the rate of false positive (FP) DCs. We present image processing methods to eliminate suboptimal metaphase cell images based on novel quality measures and to reclassify FPs by analyzing their morphological features. A set of chromosome segmentation thresholds selectively filtered out FPs, arising primarily from extended prometaphase chromosomes, sister chromatid separation and chromosome fragmentation. This reduced the number of FPs by 55% and was highly specific to the abnormal structures (≥97.7%). Image segmentation filters selectively remove images with consistently unparsable or incorrectly segmented chromosome morphologies, while image ranking sorts images according to their qualities and enables selection of optimal images in samples. Overall, these methods can eliminate at least half of the FPs detected by manual image review. By processing data to derive calibration curves and to assess samples of unknown exposures with the same image selection models, average dose estimation errors were reduced from 0.6 Gy to 0.3 Gy, without requiring manual review of DCs. During this presentation, we will use our software to demonstrate that metaphase image filtering and object selection constitute a reliable and scalable approach for biodosimetry, resulting in more accurate radiation dose estimates.

1. International Atomic Energy Agency. (2001) Cytogenetic Analysis for Radiation Dose Assessment, a Manual: Technical Reports Series. No. 405, International Atomic Energy Agency, Vienna.
2. International Atomic Energy Agency. (2011) Cytogenetic Dosimetry: Applications in Preparedness for and Response to Radiation Emergencies, International Atomic Energy Agency, Vienna.
3. Rogan, P. K., Li, Y., Wilkins, R. C., Flegal, F. N., and Knoll, J. H. M. (2016) Radiation Dose Estimation by Automated Cytogenetic Biodosimetry, Radiation Protection Dosimetry 172, 207-217.

Keywords: Bioinformatics; Centromere structure/function; Chromosomal abnormalities; Diagnostics; Public health

PgmNr 1288/W: Predicting exposure to ionizing radiation by biochemically-inspired genomic machine learning. (Poster)

Wed, Oct 18.  3:00pm – 4:00pm. Bioinformatics and Computational Approaches. Exhibit Hall, Level 1, Orlando Convention Center. 
J.Z.L. Zhao; E.J. Mucaki; P.K. Rogan.  Dept Biochemistry, University of Western Ontario, and CytoGnomix Inc., London, Ontario, Canada

Analyzing gene expression in peripheral blood mononuclear cells reveals profiles that predict radiation exposure in humans and mice by logistic regression (PLoS Med. 4:e106; PLoS ONE. 3:e1912). Using biochemically-inspired methods (Mol. Onc. 10:85-100), we derive gene signatures to predict the level of radiation exposure with improved accuracies. DNA repair genes responsive or differentially expressed upon radiation exposure and orthologs highly expressed in species resilient to radiation exposure (n=998) were analyzed by two-sampled t-tests comparing expression in individuals unexposed and exposed to radiation (150-200 cGy: humans or 50-1000 cGy: mice). Significance thresholds for including a gene in developing a signature were adjusted based on radiation dose, from p < 0.01 (50 cGy) to < 1E-14 (1000 cGy), equivalent to ~10% of genes. Support Vector Machine (SVM) signatures were derived by backward feature selection (BFS) or minimum-redundancy-maximum-relevance (mRMR) and validated using leave-one-out cross validation (LOOCV) and external datasets. GEO datasets GSE6874 and GSE10640 were used for training and testing. Signatures derived by BFS from the human patients of GSE6874 (n=78) included α) GADD45A, GTF3A, TNFRSF4, XPC and β) ATR, GADD45A, GTF3A, IL2RB, MYC, NEIL2, RBM15, SERPINB1, XPC, which both distinguished irradiated from unirradiated individuals with 98% sensitivity and 100% specificity in LOOCV. Validating these signatures on the human patients of GSE10640 (n=71) confirms that α and β are both 92% sensitive and, respectively, 94% and 96% specific. mRMR found the 10 “best” genes from the murine samples of GSE10640 (n=104) to create a signature at each radiation dose; several genes were common among signatures. Signature δ (50 cGy) included PHLDA3, BAX, NBN, CCT3, CDKN1A, CCNG1, POLK, ERCC5, GCDH, and RAMP1. Signature ε (200 cGy) included PHLDA3, LIMD1, CCT3, BAX, MS4A1, GLIPR2, BLNK, BCAR3, CDKN1A, andTFAM. Signature ζ (1000 cGy) included CCT3, SUCLG2, EI24, CNBP, PHLDA3, TPST1, HEXB, FEN1, CDKN1A, and BLNK. When validated on the murine samples of GSE6874 (n=14), each signature correctly predicted the exposure status of all mice. Our approach produces signatures with higher accuracies in cross- and external validation datasets than prior logistic regression models, with significantly improved sensitivities in detecting radiation exposure in humans. This will be useful in identifying nearly all radiation-exposed individuals in a mass casualty.

Keywords: Bioinformatics; Diagnostics; Transcriptome; Computational tools; Hematopoietic system

July 12, 2017. CytoGnomix exhibiting at 2017 American Society of Human Genetics Annual Conference

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We will be exhibiting our cytogenetics and genomics products at the upcoming American Society of Human Genetics Annual Conference in Orlando, Florida (Oct 17-21, 2017). Please visit our booth or come by to ask questions our software and reagents. Talk to us about genome interpretation with MutationForecaster, radiation dose estimation with the Automated Dicentric Chromosome Identifier, or single copy reagents for NGS capture, FISH or microarrays.  We will also be presenting 3 scientific papers at the meeting.

We  welcome inquiries about joint R & D projects and partnerships.  Contact us.

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