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myGENetiks is a service and consulting company for biomedical and genome data. We provide specialized support services for the design of biological experiments, the analysis and interpretation of data. We specialize in developing new technologies to enable scientists and physicians to get more results in less time. The company is made up of doctors and researchers from all around the world to help the scientific community. Using the experience of each of our professional teams, myGENetiks will offer you innovative and simple solutions to your scientific questions.
Made by researchers for researchers, we specialize in:
- Sequencing and genotyping of your samples.
- Genomic data processing using our certified algorithms.
- Consultancy in bioinformatics and genomic analysis.
- Discovery of disease genes linked to a specific phenotype.
- Design and construction of algorithms for the processing and analysis of genomic data.
- Bioinformatic solutions and tools to run genomic analysis in the cloud.
Our priority as a group is to help you with your research, explore all the possibilities you have at the moment and adapt them to your budget. myGENetiks provides scalable and open bioinformatics solutions which enable scientists to extract the greatest value from their research data, across a variety of applications, technologies, and industries. Our team will help you be independent, trust your genomic data analysis results to ensure that our collaboration with you has high quality results and are accepted in high impact journals.
Consultancy in bioinformatics and genomic analysis
Whether you are a dedicated researcher or just someone with a general curiosity about genetics, myGENetiks is here to provide the next generation sequencing (NGS) and microarray services for all your needs. Our team was designed to assist you in areas of difficulties, such as Bio-informatics, statistics, and data mining at the most affordable price. Contact our representatives if you want information about the use of one of our services for your research needs.
Services in bioinformatics and genomic analysis
How can we help you
Made by researchers for researchers, we specialize in:
1) Sequencing and genotyping of your samples
myGENetiks is built to provide the best products at the most affordable price through our collaborator laboratories. We provides a wide range of molecular biology services, including: DNA extraction, Sanger Sequencing, Next-Generation Sequencing, SNP Genotyping Microarrays, RNA-seq, targeted gene panels, and many others at a low cost to the entire research community.
3) Consultancy in bioinformatics and genomic analysis
We will meet with you to discuss the types of analysis and support we can provide. We will help you design your genomic experiments and incorporate the analysis of your results into your research plan.
2) Genomic data processing
Frustrated with genomic data processing? We know how painful it can be that things work well with bioinformatics. Our team of professionals will help you process your genomic data using their certified and up-to-date algorithms. Processing the genomic data correctly will be the best start of your project and the only way to make it successful.
4) Discovery of causal genes linked to a specific phenotype
Finding genomic variants that cause a particular disease or phenotype is difficult and time-consuming. Of the 100,000 variants typically found in an exome sequencing (WES), only a few of them will have medical relevance. We work with researchers (professors, doctors, post-docs and postgraduate students) to provide high-throughput sequencing analysis, genomic, metabolic and other biological data.
5) Design and construction of algorithms for the processing and analysis of genomic data
We help develop customized applications to enhance research for genomic analysis, such as: create custom algorithms, databases and/or visualization, as well as web services interfaces for databases and custom analysis tools.
6) Bioinformatic solutions and tools to run genomic analysis in the cloud
Cloud services, such as those provided by Amazon and Google, are increasingly being used by genomics researchers around the world. Cloud computing allows you to run virtual machines on remote servers, with various levels of support for bioinformatics. Our team of professionals will be able to help you start using cloud computing and training your staff.
myGENetiks will not share any personal or medical information with any person or company external to our contract (read privacy agreement).
Types of analysis we do
myGENetiks applies certificated front-edge bioinformatic workflows and tools for analyzing microarray (SNPs) and next generation sequencing data, including data handling, normalization, biomarker signature identification and classification.
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1) Whole exome/genome
Sequencing (WES/WGS)
A) Processing of initial data
- Quality control of raw data
- file processing: fastq vcf
- file processing: bam/cram fastq vcf
- Discovery of variants: SNPs/indels
B) Annotation of variants using 26 important databases in genetics.
- Location: UCSC, Ensembl and RefGene
- Importance: HGMD, OMIM, GeneCards, Geneontology, Mito-Carta.
- Classification: Polyphen2, SIFT, Mutation Taster, etc. (11 algorithms).
- Effect of variant: frameshift, nonsense, missense, etc.
- Frequency: dbSNP, ExAC (65,000 samples), EVS (6,500 samples), 1000 genomes and 5,000 exomes with phenotype processed by MyGENetiks
- Classification for non-coding regions: Encode histone marks
C) Classical analyzes using Mendelian genetics (rare diseases)
- Recessive Model
- Dominant Model
- De novo Model
- Prioritization of variants
- Manual verification of causal variants
- Pathway analysis of causal variants
D) Analysis for common diseases
- GWAS
- Gene analysis and genetic modifications associated with a disease.
E) CNV detection
- CNV discovery
F) Analysis of results with specialists
- Verification of results with specialists (Medical specialists, academic collaborators)
- Final verdict of causal variants by MyGENetiks and all his group of professionals.
2) Microarrays Analysis (SNPs)
A) Processing of initial data
- Quality control of raw data
- Data processing using 4 algorithms (Birdseye, PennCNV, Affymetrix,
- QuantiSNP)
B) Detection of CNVs
- CNV discovery using 4 algorithms.
- Quality control of CNVs and filtering.
- Importance: HGMD, OMIM, GeneCards, Geneontology, Myth-Letter.
- Classification for non-coding regions: Encode histone marks.
- Frequency: 1,258 samples of HapMap3 and 12,177 samples with phenotype processed by MyGENetiks
- Detection of population artifacts.
- Manual verification of causal CNVs linked to a specific phenotype.
C) Classic analysis:
- Quality control SNP and filtering
- Linkage for families (Merlin)
- Homozygosity mapping
- Haplotype mapping
D) GWAS
- Genotype data quality control
- Statistical analysis (linear regression)
- Genetic analysis of populations
E) Analysis of results with specialists
- Verification of results with specialists (Medical specialists, academic collaborators)
- Final verdict of causal variants by MyGENetiks and all his group of professionals.
3) RNA-seq expression analysis
A) Standard Service
- Raw data QC and clean up
- Alignment to a reference with mapping statistics
- Gene and transcript-based quantitation
- TPM/RPKM/FPKM-based quantitation
- Differentially Expressed Gene
- Clustering
- Gene Ontology
- Pathway Analysis
- Gene interaction network
B) Advanced service:
- Empalme pre-mRNA alternativo
- Alternative pre-mRNA splicing
- RNA editing
- Antisense transcript
- Novel transcripts
- Fusion genes/transcript detection
Both service will include a final project report with analysis methods, graphics, and references
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Our group of professionals have worked for more than 5 years in the field of genetics, creating their own genetic analysis algorithms. myGENetiks has incorporated their most relevant research creating "Variant Explorer Pipeline" (@Copy right: myGENetiks, 2016). It is the only product on the market that addresses all the challenges of high volume data processing: accuracy, speed, efficient storage and ease of use for research and clinical application. myGENetiks has processed successfully using our certificate algorithm more than 18,000 samples using microarrays and 9,000 samples with whole exome/genome sequencing data with different phenotypes (Autism, Mental Retardation, Microcephaly, Walker Burger, Beta Thalassemia, Congenital Sideroblastic Anemia, Centronuclear myopathy, and rare disease). "Variant Explorer Pipeline" has more than 20 publications in high impact science journals (see our list of publications).
Publication List
Discovery of disease genes using “Variant Explorer pipeline” (@Copy right: myGENetiks, 2014)
1. Joshi M, Anselm I, Shi J, Bale TA, Towne M, Schmitz-Abe K, Crowley L, Giani FC, Kazerounian S, Markianos K, Lidov HG, Folkerth R, Sankaran VG, Agrawal PB., “Mutations in the substrate binding glycine-rich loop of the mitochondrial processing peptidase-alpha protein (PMPCA) cause a severe mitochondrial disease”, Molecular Cases Studies (March 2016).
2. Riley LG, Rudinger-Thirion J, Schmitz-Abe K, Thorburn DR, Davis RL, Teo J, Arbuckle S, Cooper ST, Campagna DR, Frugier M, Markianos K, Sue CM, Fleming MD, Christodoulou J., “LARS2 Variants Associated with Hydrops, Lactic Acidosis, Sideroblastic Anemia, and Multisystem Failure”, JIMD Report, SSIEM and Springer-Verlag Berlin Heidelberg (November 2015).
3. Schmitz-Abe K**, Ciesielski SJ**, Schmidt PJ**, Campagna DR**, Rahimov F, Schilke BA, Cuijpers M, Rieneck K, Lausen B, Linenberger ML, Sendamarai AK, Guo C, Hofmann I, Newburger PE, Matthews D, Shimamura A, Snijders PJ, Towne MC, Niemeyer CM, Watson HG, Dziegiel MH, Heeney MM, May A, Bottomley SS, Swinkels DW, Markianos K, Craig EA, Fleming MD., “Congenital sideroblastic anemia due to mutations in the mitochondrial HSP70 homologue HSPA9”, Blood (October 2015).
4. Schmitz-Abe, Klaus, et al. “Homozygous deletions of non-coding DNA sequences in Autism spectrum disorder“, International Meeting for Autism Research (IMFAR), Salt Lake City, Utah, USA (2015).
5. Nakayama T, Al-Maawali A, El-Quessny M, Rajab A, Khalil S, Stoler JM, Tan WH, Nasir R, Schmitz-Abe K, Hill RS, Partlow JN, Al-Saffar M, Servattalab S, LaCoursiere CM, Tambunan DE, Coulter ME, Elhosary PC, Gorski G, Barkovich AJ, Markianos K8, Poduri A, Mochida GH., “Mutations in PYCR2, Encoding Pyrroline-5-Carboxylate Reductase 2, Cause Microcephaly and Hypomyelination”, The American Journal of Human Genetics (Abril 2015).
6. Ahmed MY, Chioza BA, Rajab A, Schmitz-Abe K, Al-Khayat A, Al-Turki S, Baple EL, Patton MA, Al-Memar AY, Hurles ME, Partlow JN, Hill RS, Evrony GD, Servattalab S, Markianos K, Walsh CA, Crosby AH, Mochida GH., “Loss of PCLO function underlies pontocerebellar hypoplasia type III”, Neurology (Abril 2015).
7. De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, Kou Y, Liu L, Fromer M, Walker S, Singh T, Klei L, Kosmicki J, Shih-Chen F, Aleksic B, Biscaldi M, Bolton PF, Brownfeld JM, Cai J, Campbell NG, Carracedo A, Chahrour MH, Chiocchetti AG, Coon H, Crawford EL, Curran SR, Dawson G, Duketis E, Fernandez BA, Gallagher L, Geller E, Guter SJ, Hill RS, Ionita-Laza J, Jimenz Gonzalez P, Kilpinen H, Klauck SM, Kolevzon A, Lee I, Lei I, Lei J, Lehtimäki T, Lin CF, Ma'ayan A, Marshall CR, McInnes AL, Neale B, Owen MJ, Ozaki N, Parellada M, Parr JR, Purcell S, Puura K, Rajagopalan D, Rehnström K, Reichenberg A, Sabo A, Sachse M, Sanders SJ, Schafer C, Schulte-Rüther M, Skuse D, Stevens C, Szatmari P, Tammimies K, Valladares O, Voran A, Li-San W, Weiss LA, Willsey AJ, Yu TW, Yuen RK; DDD Study; Homozygosity Mapping Collaborative for Autism; UK10K Consortium, Cook EH, Freitag CM, Gill M, Hultman CM, Lehner T, Palotie A, Schellenberg GD, Sklar P, State MW, Sutcliffe JS, Walsh CA, Scherer SW, Zwick ME, Barett JC, Cutler DJ, Roeder K, Devlin B, Daly MJ, Buxbaum JD., “Synaptic, transcriptional, and chromatin genes disrupted in autism”, Nature (Nov 2014).
8. Schmitz-Abe, Klaus, et al. “Homozygous deletions of non-coding DNA sequences in Autism spectrum disorder“, American Society of Human Genetics, San Diego, USA, 64th annual meeting, (2014).
9. Agrawal PB, Joshi M2, Marinakis NS, Schmitz-Abe K, Ciarlini PD, Sargent JC, Markianos K, De Girolami U, Chad DA, Beggs AH., “Expanding the Phenotype Associated With the NEFL Mutation: Neuromuscular Disease in a Family With Overlapping Myopathic and Neurogenic Findings”, JAMA Neurology (September 2014).
10. Chakraborty PK**, Schmitz-Abe K**, Kennedy EK, Mamady H, Naas T1, Durie D, Campagna DR, Lau A, Sendamarai AK, Wiseman DH, May A, Jolles S, Connor P, Powell C, Heeney MM, Giardina PJ, Klaassen RJ, Kannengiesser C, Thuret I, Thompson AA, Marques L, Hughes S, Bonney DK, Bottomley SS, Wynn RF, Laxer RM, Minniti CP, Moppett J, Bordon V, Geraghty M, Joyce PB, Markianos K, Rudner AD, Holcik M, Fleming MD, “Mutations in TRNT1, encoding the CCA-adding enzyme, cause congenital sideroblastic anemia with B cell immunodeficiency, periodic fevers and developmental delay (SIFD)”, Blood (September 2014).
11. Campagna DR**, de Bie CI**, Schmitz-Abe K**, Sweeney M, Sendamarai AK, Schmidt PJ, Heeney MM, Yntema HG, Kannengiesser C, Grandchamp B, Niemeyer CM, Knoers NV, Swart S, Marron G, van Wijk R, Raymakers RA, May A, Markianos K, Bottomley SS, Swinkels DW, Fleming MD., “X-linked sideroblastic anemia due to ALAS2 intron 1 enhancer element GATA binding site mutations”, American Journal of Hematology (March 2014).
12. Sankaran VG, Joshi M, Agrawal A, Schmitz-Abe K, Towne MC, Marinakis N, Markianos K, Berry GT, Agrawal PB. “Rare complete loss-of-function provides insight into a pleiotropic genome-wide association study locus”, Blood (November 2013).
13. Schmitz-Abe, Klaus, et al. “Family structure is predictive of genetic architecture in autism spectrum disorders“, American Society of Human Genetics, Boston, USA, 63th annual meeting, (2013).
14. Ceyhan-Birsoy O, Agrawal PB, Hidalgo C, Schmitz-Abe K, DeChene ET, Swanson LC, Soemedi R, Vasli N, Iannaccone ST, Shieh PB, Shur N, Dennison JM, Lawlor MW, Laporte J, Markianos K, Fairbrother WG, Granzier H, Beggs AH., “Recessive truncating titin gene, TTN, mutations presenting as centronuclear myopathy”, Neurology (August 23, 2013).
15. Bartnikas TB, Wildt SJ, Wineinger AE, Schmitz-Abe K, Markianos K, Cooper DM, Fleming MD., “A Novel Rat Model of Hereditary Hemochromatosis Due to a Mutation in Transferrin Receptor 2” Comparative Medicine, Volume 63, Number 2, pp. 143-155 (January 2013).
16. Yu TW1, Chahrour MH, Coulter ME, Jiralerspong S, Okamura-Ikeda K, Ataman B, Schmitz-Abe K, Harmin DA, Adli M, Malik AN, D'Gama AM, Lim ET, Sanders SJ, Mochida GH, Partlow JN, Sunu CM, Felie JM, Rodriguez J, Nasir RH, Ware J, Joseph RM, Hill RS, Kwan BY, Al-Saffar M, Mukaddes NM, Hashmi A, Balkhy S, Gascon GG, Hisama FM, LeClair E, Poduri A, Oner O, Al-Saad S, Al-Awadi SA, Bastaki L, Ben-Omran T, Teebi AS, Al-Gazali L, Eapen V, Stevens CR, Rappaport L, Gabriel SB, Markianos K, State MW, Greenberg ME, Taniguchi H, Braverman NE, Morrow EM, Walsh CA, “Using Whole-Exome Sequencing to Identify Inherited Causes of Autism”, Neuron, Vol. 77, Issue 2, 259-273 (January 2013).
17. Schmitz-Abe, Klaus, et al. “Identifying Autism Loci using Homozygosity Analysis and Copy Number Variation Analysis“, American Society of Human Genetics, San Francisco, USA, 62th annual meeting, (2012).
18. Schmitz-Abe Klaus, et al. “Integrated pipeline for copy number variation, linkage and homozygosity, aids interpretation of variants identified through Next-Gen sequencing“, American Society of Human Genetics, 61th annual meeting, Montreal, Canada, (2011).
More information about publication: https://www.researchgate.net/profile/Klaus_Schmitz-Abe/
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