Whole Exome and Genome Sequencing

​Our entire DNA consists of approximately 20,000 genes. Genes are packed on chromosomes. A person usually has 23 double chromosomes or 46 chromosomes in total. This entire DNA collection is called a genome. The examination of the packed state, namely the chromosomes, is done by Cytogenetic methods by Medical Genetics.

Non-functioning genes can cause disease. There are different ways to study DNA. Usually a technology called sequencing is used. Sequencing reads “reads“ each letter of DNA and finds changes (variations or mutations) in our genes that may cause disease or affect a disease risk. The so-called DNA sequencing method is an advanced technique used to test for genetic disorders in the sequence of DNA building blocks (nucleotides / bases) in the individual's genetic code. There are two methods for identifying genetic variations in the individual or patient's DNA sequence. These include: All exogenous sequencing (WES) and Whole genome sequencing (WGS). It is increasingly used in health services and research; Both methods are based on new technologies that allow rapid sequencing of large amounts of DNA. These approaches are known as Next Generation Sequencing (NGS).

The original sequencing technology (the name of the scientist who developed it, Frederick Sanger), called the Sanger sequence, was a discovery that helped scientists identify the human genetic code, but it was time-consuming and expensive. The Sanger method has been automated to make it faster and is now used to sort short DNA fragments in laboratories, but sequencing can take years to process a person's DNA (known as the person's genome). NGS has stepped up the process (for a human WGS) while lowering the cost.

With the next generation of sequencing, it is now possible to sequester large amounts of DNA, such as all parts of the whole Genome or DNA of the individual, which instructs the protein to produce protein - in a short time and at an affordable price.

All exogenous sequencing is sequencing all the exosomes that encode the whole exome protein, ie the protein that is thought to constitute 1% of the genome. This method allows the study of genetic variations (mutations) in the protein coding region of all genes, rather than just a few selected genes. Since most of the known mutations that cause the disease occur in exons, it is thought that all exogenous sequencing is an effective method to identify possible mutations that cause disease.

With Whole Genome Sequencing, a great deal of genetic information can be closely looked at by sequencing or "reading" all bases in DNA (genome). The sequence of the whole genetic code of a person is called whole genome sequencing. Researchers have found that DNA variations in intron regions between the exons outside the exon can affect gene activity and protein production, and may lead to genetic defects. This method is recommended in cases where all exsomposition is performed and the results are normal.

Sequencing of Gene or Target Regions. Since the genome is much larger, exome can be sequenced at a lower cost and at a greater depth (number of readings of a particular nucleotide). Larger depth provides more confidence in rarely detected low frequency or first-time changes. In some cases, special panels can be used, which gene panels contain a number of selected genes associated with diseases previously suspected by your doctor, or mutations that contribute to the formation of diseases. The sequencing of the selected genes and target regions can be sequenced with lower costs and even more depth due to the shorter readings.

While more genetic alterations than the sequencing of the gene or target regions can be detected by whole exocrine and whole genome sequencing, the importance of most of these changes is unknown. Since all genetic changes do not affect health, it is difficult to predict whether defined variants are disease-related.

All the exom and all genome sequencing that lead the clinicians to the diagnosis are also valuable tools for researchers.



What is Microarray?

Microarray, Array Comparative Genomic Hybridization (a-CGH) is a high-tech technique used to detect small add-ins and small drop-outs that cannot be observed by a microscope. With this method, chromosome or chromosome regions increases and decreases can be detected in the whole genome. In cases of suspicion of DNA content changes of deletion or duplication which is less than 5Mb where cytogenetic methods (see Cytogenetics) are insufficient can be are examined at high resolution, therefore it is quite reliable.

When Microarray method is needed?

​It is mostly directed at children and can be used in the diagnosis of mental and gender related or physical development disorders. aCGH method is possible to use in prenatal and postnatal period. Preimplantation genetic diagnosis (PGD) is a method used to increase treatment success and decrease pregnancy losses in couples with recurrent miscarriage, recurrent failed in-vitro trials and repetitive failures.

NIPT Test

Non-invasive prenatal test (NIPT), also called non-invasive prenatal screening, is a method of determining the risk of a fetus being born with certain genetic abnormalities. This test analyzes free fetal DNA fragments circulating in the blood of a pregnant woman. The mother's blood circulation during pregnancy involves the free DNA mixture from the mother's own cells and the placenta. The placenta is a tissue of the uterus that connects the fetus and the mother's blood flow. DNA in placental cells is generally the same as the DNA of the fetus. Analysis of placental DNA provides an opportunity for early detection of certain genetic anomalies without damaging the fetus.

NIPT is commonly used to detect the presence of common chromosomal number disorders (excess or lack of chromosomes). NIPT is primarily used to detect anomalies of sex chromosomes in Down syndrome (trisomy 21 caused by extra 21 chromosome, trisomy 18 (caused by extra 18 chromosomes), trisomy 13 (caused by extra 13 chromosome), X and Y sex anomalies ( or male, sex abnormalities are reported in predicted cases). There are also extended NIPT tests, including cystic fibrosis, hemophilia, DiGeorge, Angelman, Prader Willi's syndrome etc., in addition to the above-mentioned general abnormalities. it is possible to screen close to 70 diseases.


Until now, the only way to control your baby's DNA was to take a sample of amniotic fluid (Amniocentesis), Cord blood (CS) or placenta tissue (CVS). There is a risk that all three of them will have a low rate or cause complications. NIPT, on the other hand, requires noninvasively taking blood from the pregnant woman's arm and does not pose any risk for the fetus.

Because NIPT is more reliable than screening tests such as first trimester screening or quadruple testing (blood test, nuchal translucency, etc.), it can recover many women from invasive procedures such as unnecessary Amniocentesis or CVS.

If your test result is negative, the risk of anomaly in your baby is low, and if it is positive, your doctor may recommend further testing (CVS, Amniocentesis, CS).

NIPT is a screening test, ie it does not give a definite conclusion whether a fetus has a genetic disorder. The test can only predict whether the risk of having a certain anomaly increases or not. The sensitivity of the test depends on the anomaly. Sometimes placental DNA may be different from fetus DNA, so the results for decision-making should not be used alone, without clinical information

In some cases, false positives (showing the risk of genetic anomalies even if the fetus is not actually affected) may be false negative (in some cases the fetus shows that the risk of a genetic abnormality is not increased even though the fetus is indeed chromosomal anomaly). Because this method analyzes both the fetus and the mother's free DNA, sometimes the test can detect the genetic condition in the mother. In order to define fetal chromosomal abnormalities, the fetus should have sufficient free DNA (4% minimum) in the bloodstream of the mother and this ratio corresponds to the 10th week of pregnancy. The free DNA rate of the fetus may lead to inability to test or false negative results. Low rate causes include very early testing, sampling errors, maternal obesity and fetal abnormalities.

Currently, NIPT is only used for women with high risk pregnancies. Many experts think that this method will be a standard test instead of more risky screening tests a day. This test should be performed once, at any time between 10 and 22 weeks (sometimes 9 weeks). The test can be performed to all women, but it is recommended routinely to women over the age of 35 and at high risk for genetic abnormalities.

Cytogenetic

Our DNA containing about 20 000 genes, consisting of 3 billion base pairs, constitutes our genetic code, is packed into 23 pairs of chromosomes within the cell. Cytogenetics is a genetic method that investigates the numerical and structural anomalies of these chromosomes. Cytogenetics is the evaluation of chromosomes by culturing any living tissue in the laboratory (blood, bone marrow, etc.), inducing the division of cells which are visible in the light microscope, in terms of fracture, missing or redundancy. Some chromosomal changes may be a sign of a genetic disease or condition or some types of cancer. With cytogenetic test results, it is possible to diagnose the disease or condition and to help plan of the treatment or to monitor how well the treatment works. Cytogenetic studies begin by removing all chromosomes from the nuclei of cells. These chromosomes are then transferred to glass slides, painted with special paints and examined by making them visible under the microscope. Different staining and banding techniques can be used to diagnose the changes detected during the examination (NOR banding, C banding etc.).

Using computer software, the images of chromosomes in the slides are taken and the picture is divided into pieces, so that the pairs of chromosomes can be matched according to the size and the the way they painted as indicated on the ideogram. Each chromosome pair is assigned a special number (1 to 22, plus X and Y) to prepare the karyotype of the individual.


There are many diseases that can be diagnosed by examining the karyotype of the individual. For example, Down's syndrome in which an individual has extra chromosome 21 can be identified by cytogenetic studies. In a karyotype, instead of a pair of chromosomes if there are three chromosomes this is called "trisomy". It can also be determined by this method that a woman has only one X chromosome as in the case of Turner syndrome. If there is only a chromosome instead of a pair, it is called "monozomy".

Sometimes a chromosome fragment and sticks to another chromosome. This is called "translocation". As an example of a disease caused by translocation, a part of chromosome 9 breaks down and connects to chromosome 22 called chronic myeloid leukemia (CML). Chromosome 8 to chromosome 14 translocation called Burkitt lymphoma. The cause of the disease caused by translocations is usually loss of gene at breakpoints or at the point of attachment of a specific gene that converts normal cells into tumor cells. Occasionally, transloxion occurs as a balanced translocation that does not cause loss or activation of the gene, which is harmless to the individual but may cause recurrent pregnancy losses.

Moleküler Genetik

  • • Sanger Sequence Analysis
  • • New Generation Sequence Analysis
  • • Quantitative Real Time PCR
  • • Expression Analysis
  • • STR Analysis
  • • PCR-Gel Electrophoresis
  • • Multiplex PCR vs.

Molecular Cytogenetics

It consists of a combination of molecular cytogenetics, molecular genetics and cytogenetics (see Cytogenetics); It is a method for detecting the genetic anomaly that causes disease, that is, the structure of chromosomes, loss or increase in genomic DNA by using various materials (DNA probes) that are capable of recognizing different parts of our DNA. An example of this method is the so-called fluorescent in situ hybridization (FISH) technique, in which DNA probes are labeled with different colored fluorescent labels to visualize one or more specific regions of the genome.  There are also several subtypes of the FISH method that serve different purposes:

Locus-specific probes are designed to bind to a specific region of a chromosome. And the loss or increase of this part, depending on whether there is binding, is defined.

Probes that stain all chromosomes are a mixture of smaller probes, each of which binds to a different sequence along the length of a given chromosome. In this method called Multicolor-FISH (M-FISH), each chromosome can be labeled in its own unique color. The result is a full color map of the karyotype. This method is primarily useful for examining chromosomal structural abnormalities, for example, when a piece of chromosome is connected to the end of another chromosome, the chromosome marked with 2 different dyes, not a single dye, will be seen.

Microarray, the Array Comparative Genomic Hybridization (a-CGH) method (see Microarray) can also be considered as a kind of molecular cytogenetic method

Patient examination

Physical examination is an indispensable tool that provides support to the diagnosis with the genealogical analysis of Medical Genetics, family and patient history information. Physical examination in Medical Genetics aims to identify a unifying etiology for unrelated birth defects, developmental problems, or other abnormal findings in a fetus, child or adult, and to facilitate the pathway to diagnosis. Accurate prognostic and repeat risk estimates, clinical treatment facilities and genetic counseling are only possible by making an accurate diagnosis.

Understanding the pathogenesis of a patient's problems provides families with psychological support to cope with the guilt of “why” their children have this problem. It also enables their families to be directed to communicate with appropriate support groups and to follow up on current treatment methods.

In physical genetics, physical examination is based on the art of dysmorphology, which is based on defining abnormal findings. Detailed analysis of body structure is used to detect potential deviations from normal embryological development. Although genetic physical examination is the same as general medical examination, body structure, size, proportion, symmetry, etc. much more attention is paid to the parameters. Indeed, the precise observation and accurate definition of all physical characteristics is the cornerstone of the genetic dysmorphology examination.

In our center, patient examination is performed by Medical Genetic specialists. Based on this examination, appropriate laboratory tests for genetic diagnosis are selected, finalized and interpreted.

Laboratory Design, Installation and Operation Services

DETA-GEN; laboratory design and a comprehensive service to meet your business needs. It provides comprehensive technical advice to ensure that laboratories meet their needs accurately for the analysis required.

Laboratory Design

We design the laboratory in accordance with the objectives of the ordering unit and fully meet the licensing criteria

Laboratory Installation

We carry out laboratory installation in accordance with the design that is pre-designed and approved by the ordering unit.

Laboratory Management

If necessary, we provide personnel in laboratories to provide the necessary tests and analysis. We also provide support through counseling. Invoicing tests. In case of insufficient infrastructure, we ensure that the necessary analysis stages are performed in our center.

    Laboratory Services

  • • Array - Comparative Genomic Hybridization
  • • Deletion Analysis
  • • Sequence Analysis
  • • Tissue Culture
  • • Floresan In Situ Hibridizasyon (FISH)
  • • Quantitative Floresan PCR
  • • Quantitative Real Time PCR and Expression Analysis
  • • Comparative Genomic Hybridization
  • • Methylation Studies
  • • Microarray Expression Studies
  • • Multiplex Ligation-dependent Probe Amplification (MLPA)
  • • Multipleks PCR
  • • PCR - Gel Electrophoresis
  • • Real Time PCR-Mutation Tests
  • • Cytogenetic
  • • SNP Mikro-Array
  • • STR Analysis
  • • New Generation Sequencing

Genetic Counseling

  • • How can hereditary diseases affect individuals or their families?
  • • How can family and individual history affect the likelihood of disease occurrence or recurrence?
  • • Which genetic test is appropriate and what or may it not show?
  • • How to make the most appropriate choices?

Who is a Genetic Consultant? Genetic counselors are medical professionals with unique degrees and experience in the fields of Medical Genetic expertise and counseling. Genetic consultants; By providing risk assessment, they provide support to individuals and families who are at risk or diagnosed for various hereditary conditions. Genetic counselors interpret genetic tests, provide supportive counseling, and serve as patient advocates.

Genetic consultants work in many fields of medicine including cancer, prenatal, pediatric and adult. Some genetic consultants specialize in areas such as cardiology, neurology and infertility. In addition, some genetic consultants work outside of clinical practice in research, education, public health, and industrial settings.

  • • Assisted Reproductive Technology / Infertility Genetics
  • • Cancer Genetics
  • • Cardiovascular Genetics
  • • Genetics of Cystic Fibrosis
  • • Genetics of Fetal Intervention and Therapy
  • • Genetics of Hematology
  • • Metabolic Genetics
  • • Neurogenetics
  • • Pediatric Genetics
  • • Personalized Medical Genetics
  • • Prenatal Genetics
  • • Post-Mortem Genetic Test

You can have a genetic test without seeing a Medical Genetic Specialist or counselor, the doctor you are following can make a test request and give you results. However, if your doctor does not know enough about genetics,           you may experience unnecessary worries with confusion. , you may have other questions that cause you to worry. Genetic counselors will advise you of hereditary diseases and conditions.           or further information about how it may affect your family. Genetic consultants can follow rapidly growing discoveries in genetics           and if new suggestions arise or if something new is discovered about genetic mutations, they can contact you.

Medical Genetics specialists and consultants at our center are always available to interpret test results and to easily explain information to patients.

Scientific Projects

  • • Research and presentation of predicted molecular genetic mechanisms and pathways related to your project
  • • Reviewing the literature related to your project and presenting the research topic and / or topics including sources
  • • Design appropriate genetic and epigenetic based (polymorphism, gene sequencing, mRNA expression, DNA methylation, etc.) molecular methods
  • • Design of genetic laboratory methods
  • • Providing laboratory analysis (Primary-oligo design and setup, Sequence Analysis (Sanger and YND), Real Time PCR, Microarray Applications etc.)
  • • Performing statistical analysis of your obtained and / or available results
  • • Designing visuals (diagrams, diagrams, graphs, etc.) for easy understanding of your work
  • • Presenting the data obtained as a result of your research in the form of a discussion by comparing the literature and specifying the source
  • • Designing your project as an article
  • • Organizing resources quickly using library programs (EndNote, etc.)
  • • Translation and / or editing of your work in English
  • • Evaluation and reduction of plagiarism percentage
  • • Providing consultation on paperwork and magazine selection related to your project
  • • Submission of the article to journals and follow-up of the evaluation process
  • • Academic presentation and design of posters

Our Publications

    1.

    Researcher: Ahmet Okay Caglayan, Fatma Demiryilmaz, Isilay Ozyazgan, Hakan Gumus
    Release date: November 23, 2009
    Title:MEFV gene compound heterozygous mutations in familial Mediterranean fever phenotype:a retrospective clinical and molecular study
    Journal: Nephrology Dialysis Transplantation, 25(8), 2520–2523
    Journal Impact Factor: 4.085 (2015)
    DOI: 10.1093/ndt/gfp632
    PMID:19934083
    Connection: Go To the Article

    2.

    Researcher: Ahmet Okay Caglayan, Isilay Ozyazgan, Fatma Demiryilmaz, Munis Dundar
    Release date: October-December 2010
    Title: Cytogenetic Results of Patients with Infertility in Middle Anatolia, Turkey: Do Heterochromatin Polymorphisms Affect Fertility?
    Journal: Journal of reproduction & infertility. 11(3): 179–181.
    Journal Impact Factor: -
    PMID: 23926487
    Connection: Go To the Article.

    3.

    Researcher: Munis Dundar,Gordon Lowther,Hasan Acar,Selim Kurtoglu,Fatma Demiryilmaz,Mustafa Kucukaydin
    Release date: January – March 2001
    Title: A case of ambiguous genitalia presenting with a 45,X/46,Xr(Y)(p11.2;q11.23)/47,X,idic(Y)(p11.2),idic(Y)(p11.2) karyotype
    Journal:: Annales de génétique (European journal of medical genetics), 44(1), 5-8
    Journal nin Etki Faktörü (Impact Factor): 2.004 (2018)
    DOI: 10.1016/S0003-3995(00)01034-0
    PMID:11334610
    Connection:Go To the Article.

    4.

    Researcher: Munis Dundar,Fatma Demiryilmaz, Ilhan Demiryilmaz, Sefer Kumandas, Kuddusi Erkilic, Mustafa Kendirci, Mehmet Tuncel, Isilay Ozyazgan, John L Tolmie
    Release date: January 1997
    Title: An autosomal recessive adducted thumb‐club foot syndrome observed in Turkish cousins
    Journal:: Clinical genetics, 51(1)
    Journal Impact Factor: 3.512 (2018)
    DOI: 10.1111/j.1399-0004.1997.tb02417.x
    PMID: 9084938
    Connection: Go To the Article.

    5.

    Researcher:Munis Dundar, Kuddusi Erkiliç,Fatma Demiryilmaz, Mustafa Küçükaydin, Mustafa Kendirci, Hamit Okur, Ahmet Kazez
    Release date: April 1996
    Title: Congenital alacrima in a patient with G (Opitz Frias) syndrome
    Journal:: Human Genetics, 97(4), 540–542
    Journal Impact Factor: 3.930
    DOI: 10.1007/bf02267083
    PMID: 8834259
    Connection:Go To the Article.

    6.

    Researcher: Ahmet Okay Çağlayan, Işılay Özyazgan,Fatma Demiryilmaz, Mahmut Tuncay Ozgun
    Release date: July 21, 2010
    Title: Are heterochromatin polymorphisms associated with recurrent miscarriage?
    Journal:: The Journal OF Obstetrics and Gynaecology Research, 36(4), 774-776
    Journal Impact Factor: 1.091
    DOI: 10.1111/j.1447-0756.2010.01207.x
    PMID: 20666944
    Connection:Go To the Article.

    7.

    Researcher: Shaza W. Shantier, Hashim E. Elmansi, Mihad E. Elnnewery, Hind K. Osman, Fatima A. Abdelrhman, Ahmed A. Eltay, Einas M. Yousif, Alaa I. Abdalla, Rawan A. Elamin, Howina S. Fadol, Isam-Aldin A. Osman, Afra A. Fadl Alla,Mohamed A. Hassan  
    Release date: February 16, 2019
    Title:Computational Analysis of Single Nucleotide polymorphisms (SNPs) in Human T-Cell Acute Lymphocytic Leukemia Protein 1 (TAL1) Gene/ Comprehensive Study.
    Journal::International Journal of Multidisciplinary and Current Research,Vol.7 (Jan/Feb 2019 issue),33-41
    Journal Impact Factor: -
    Connection:Go To the Article.

    8.

    Researcher:Sulafa Mohamed Eltaher, Abeer Babiker Idris, Mahmoud A. H, Mawadah Yousif Mohamed Yousif, Nouh Saad Mohamed, Muzamil M. Abdel Hamid, Kamal Elzaki Elsiddig, Galal Mohammed Yousif,Mohamed A. Hassan 
    Release date: March 9, 2019
    Title: Genetic analysis of TP53 gene mutations in exon 4 and exon 8 among esophageal cancer patients in Sudan
    Journal::Preprint
    Journal Impact Factor:-
    DOI:10.1101/572214
    Connection:Go To the Article.

    9.

    Researcher: Nidal Essa, Enas A. Osman, Hadeel M. Yousif, Kutuf A. Albushra, Amel Nasir Eltayeb Ali, Tebyan Ameer Abdelhameed Abbas,Mohamed A. Hassan
    Release date: 2019
    Title: Comprehensive Computational Analysis Revealed Thirteen Novel Mutations in Human FSH-B gene Related to PCOS.
    Journal::American Journal of Bioinformatics Research, 2019; 9(1): 11-21
    Journal Impact Factor:-
    DOI:10.4149/BLL_2019_016
    Connection:
    Go To the Article