Consultant Office for Medical Services - COMS€¦ · the knowledge and tools necessary to become successful in a fast paced and constantly evolving environment. Our international

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Consultant Office for Medical Services

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Introduction

COMS aspires to provide companies, organizations and individuals with the knowledge and tools necessary to become successful in a fast paced and constantly evolving environment. Our international team comes from diverse backgrounds with experience in diverse sectors. We use this diver-sity and knowledge to create a unique and innovative curriculum of train-ing and consulting services to fit the needs of any company, organization, or individual.

COMS strives to become a leading provider of capacity building, train-ing and consulting services. We envision to provide excellent solutions in medical and halth care, research, education and scientific publication practices. COMS commited to foster this vision and become a leading consultancy in health and wellness, education and technology. We are commitmented to create partnerships that offers access to a wide range of health care options.

Vision

Mission

COMS aims to provide the professional services to its clients tailored to the need of individual or organization backed by consistent quality practice, scientific knowledge, state of the art technology and methods, products and other miscellaneous services. No wonder then, COMS have estab-lished its credentials in diverse areas of research, education, training and skills. Our experienced staff is highly capable of building a sustainable and productive business with achievable results, ensure success and pro-actively contribute in maximizing efficiency. To back this, we have an efficient consultation experience, developed quality training, workshop, continuing education rigorous programs and achieved excellent skills in scientific and research publications. COMS mission is results and reliability by investing in relationships.

LocationThe workshops and training programs will be held in College of American Pathologist (CAP) accredited labora-tories of the COMS at King Abdul Aziz University.

Documents and CertificateParticipants who complete the theo-retical and practical parts will be awarded a certificate of completion accredited by the Saudi Commission for Health Specialties.

Fees and Registration

Order to participate in the work-shop; you need to register online. Payment of the fees is part of the electronic registration applica-tion and can be made by transfer-ring the fees to account number in COMS web site. Registration is on the basis of first come first served; therefore early registration is highly recommended. The receipt will also be uploaded. Fees will also include break refresh-ments, lunch, all workshops materi-als and documentation.

The training and the workshops are supervised by a group of a highly qualified consultant, physicians and specialized teaching staff from the College of Medicine and Applied Medical Sciences.

Supervisory and Consultancy Committee

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4 Consultant Office for Medical Services

Workshops

• Concept of cytoge-

netic

• Types of microscopes

and its application

• Chromosomal Analysis

Course Outline

APPLICATION OF CLINICAL CYTOGENETICS

ObjectiveApplicants will learn about the importance and use of the cytogenetics in the modern medical practice. You will be provided with an in-depth knowledge about the clinical cytogenetics applications.

• Describing Banding and no-

menclature (ISCN)

• Cytogenetic Result, Report-

ing and Interpretation

• Application of cytovision

image analysis

• Genetic Counseling

•Sample processing, prin-ciple of cell culturing and isolation of lymphocytes principle of lymphocyte harvesting, slide prepa-ration, slide staining, microscope analysis and karyotyping preparation

Workshops


Workshops

• Clinical Application of

Fluorescence In Situ Hy-

bridization in situ Hybridi-

zation in Medical Practice

Course Outline

APPLICATION OF FLUORESCENCE IN SITU HYBRIDIZATION

FISH is commonly used in clinical setting for diagnosis and studying inher-ited genetic diseases. Applicants will learn how to get valuable information/data about the chromosomal status for any human disease or organism, analyze the data and report them by imaging.

• Nomenclature (ISCN) of

FISH Result

• Result Interpretation and

Reporting using different

types of FISH probe

• Probe Labelling

• Overview of Computer-

ized Image Analysis

• Microdeletions Syn-

dromes FISH Application

Objective

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Participants will have the opportunity to learn the principles of the Poly-merase Chain Reaction technique as well as its applications in genetic diagnosis. The PCR applications are ranging from gene amplification, mu-tation screening to SNPs detection.

APPLICATION OF PCR IN DIAGNOSTIC MOLECULAR GENETICS

Objective

Course Outline

•PCR Optimization

•DNA Extraction

•PCR Amplification

•PCR and thermal

cycling

•Gel Electrophoresis

•Restriction fragment

length polymorphism

(RFLP) and its applications

•Restriction enzyme pro-

cessing of amplified PCR

product

•PCR primer designing

•RT-PCR

•UV Transillumination

using documentation

system and gel interpre-

tation


Workshops

• Overview of DNA se-

quencing

• Applications of se-

quencing

• Isolation of DNA from

whole blood

Course Outline

APPLICATION OF DNA SEQUENCING

ObjectiveIn this advanced workshop, applicants will understand how dideoxy-

nucleotides can be used to obtain DNA sequencing. You will learn how sequence reading can be automated using Fluorescent ddNTPs. You will also be able to read the sequence from the gel chromatogram. Moreo-ver, you will learn how to detect the sequence errors and how to apply such high throughput DNA sequence to understanding human diseases.

• Types of mutations and

other applications of a ge-

netic analyzer

• Sequencing data analysis

and storage

• PCR amplification of

DNA using fragment spe-

cific PCR primers

• Gel Electrophoresis

• Cycle sequencing

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Course Outline

HIGH THROUGHPUT DNA SEQUENCING

Objective

In this advanced workshop, you will understand how dideoxynucleotides can be used to obtain DNA sequencing. You will learn how sequence reading can be automated using Fluorescent ddNTPs. You will also be able to read the sequence from the gel chromatogram. Moreover, you will learn how to detect the sequence errors and how to apply such high throughput DNA sequence to understanding the human diseases.

• Introduction to NGS SOLID workflow

• Fragment library prep-aration

• ePCR demonstration

• Enrichment process

• Slide preparation and loading

• Instrument preparation for run and ICS

• Color space review


Workshops

• The latest generation of

cytogenetic microarray

• Measurement of quantity

and quality of nucleic acid

• Overview of the gene ex-

pression assay workflow on the

Affymetrix gene chip system

part1 (cRNA purification)

Course Outline

• Overview of the gene expres-

sion assay workflow on the Affy-

metrix gene chip system, part III

(hybridization, wash and scan)

• Structure disorders both in

autism and intellectual disability

using cytoscan and CGH array

• Overview of the array CGH

workflow using the Agilent

platform

• Chromosomal microarray ap-

proach to abnormal reads

• Overview of array CGH

workflow

• Overview of the gene ex-

pression assay workflow on the

Affymetrix gene chip system,

part II (cDNA purification)

AFFYMETRIX /AGILENT MICROARRAY GENE CHIPSHealthcare

Objective

Applicants will learn how you can do expression profiling of a DNA or RNA. The goal is to identify genes that are regulated or expressed in a particular tissue. You will learn how to correlate the results to the signalling pathway(s).

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Course Outline

POWER OF BIOINFORMATICS

Bioinformatics is an integral entity of modern science used to analyze huge data (genomic, proteomic or metabolomics) generated by high throughput technologies like Next Generation Sequencing and Microarray.

• Introduction to Bioinformatics• Microarray Data analysis Microarray technology and statistical analysis Detecting differentially expressed genes• Biological Interpretation of Results Genomic integration and visualization of results Pathway analysis Functional Annotation and Gene Ontology• “R” programming for Sequence Analysis (Bioinformatics) Structural Genomics and Structure Visualization Protein Data Bank Retrieving protein sequence along with structural coordinates Protein Structure Visualization • Molecular Modeling and Docking Protein-Ligand Interaction Docking and Modeling of Proteins


Workshops

• Application of flow cy-

tometry in leukemia and

lymphoma

• Staining of cell line sam-

ples for multicolor analysis

of cell surface antigens

Course Outline

APPLICATIONS OF FLOW CYTOMETRY

Objective

Flow cytometry is important for sorting out live cells from various solid and liquid tissue sources. Applicants will learn how to sort out these cells and use them for downstream characterization analysis and how to culture them using specific affinity methods.

• Cell cycle analysis

• Apoptosis

• Cell proliferation

• Multiparametric analysis

on a flow cytometer

• Demonstration of

acquisition and analysis

software

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• Biobank institution and banking discipline: from Human Genome project to biobanks• Definition of biobanks, importance & govern-ance • Biobank: Logistics & hu-man resources

Course Outline

Introduction Biobanking Toward Precision Medicine & Sustainable Healthcare is an advanced international workshop focusing on the development of biobank as an important pillar of personalized medicine that strongly support scientific progress, biomedical innova-tion and sustainable healthcare. In fact, biobank is a core platform dedicated to recruit, process cryopreserve, store, and distribute human and non-human bio specimen in se-quence to provide healthcare researchers with high quality and clinical annotated bio specimens to facility their research discoveries in order to improve clinical outcomes and therefor the health services in the Kingdome of Saudi Arabia Given the development of bio banking as a scientific endeavor over the past decade, and the emergence of in-ternational technical and ethical/regulatory standards, this workshop will be a valuable opportunity for the GenaTi biobank to upgrade its management and establish a wide national and international network with stakeholders, experts and industries involved in bio banking. The main topics covered in this workshop are but not limited to: • Definition of biobanks, importance, governance, types and biospecimen processing cycle• Role of biobank in the establishment of ethics, privacy & confidentially protection as wee as biodata security, standards to enhance trustable biomedical research and healthcare.• Showcase the biobank requiems in terms of logistics and human resources• Explain the purpose and principles underlying informed consent, the types of consent and special considerations during the consent process• Concept of Biodata and research data management and sharing• Biobanking education awareness toward sustainable healthcare

• Biospecimens manage-

ment (SOPs)

• The concept of Biodata,

research data management

and responsible data sharing

• Biobanking education and

awareness toward sustain-

able healthcare

• Biobank types and networking• Biobanking ethics, pri-vacy & confidentially • Biobanking: Toward Effective Healthcare System • Purpose and principles underlying informed consent

Biobanking Toward Precision Medicine & Sustainable


Workshops

HOW TO PUBLISH IN HIGH-IMPACT JOURNAL

ObjectiveIn this workshop, the applicant will learn to prepare your work and results for publication. We will show you how to carry out effective strategies and techniques in writing up different types of articles.

Course Outline

• Writing for publication, basic skills

• Articles writing up skills

• Writing for publication, Advanced skills

• The publisher’s per-spective on increasing publications impact and reach

• Overview of publishing in npj Genomic medi-cine

• Behind the scenes at Nature-demystifying the editorial process

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Course Outline

Applications of Immunohistochemistry workshop

Participants in this workshop will receive a comprehensive understanding of the IHC principles reinforced by a hands-on laboratory practice to iden-tify the histopathological features and/or biomarkers of diseases.

• Basics of Histology & Cytology• Histology Staining Methods• Immunohistochemistry (IHC), • Antibodies: overview, types• Tissue Microarray (TMA) Technology• IHC Scoring Systems • Expression Patterns Profiling & Scoring Systems• Manual IHC Scoring (light microscope), Subjective method(s) and Objec-tive method(s)

Objective


Workshops

Principle and Application of cell cultureObjective Applicants interested in cell-based research applications will understand the basics of cell culture and have hands-on experience to enable them to conceptualize and design a cell-based research experiment.

Course Outline• Media/ Reagents preparation• Labelling and storage • Handling micropipettes• Handling of cell culture related equipment(s)• Describing Banding and nomenclature (ISCN)• Autoclaving• Cell Thawing • Cell counting • Cell Imaging • Trypsinization• Cell plating / Cell seeding• Cell Freezing• CD Marker Assay• Cell seeding for MTT assay• Cell Proliferation (MTT assay)• Cell Cycle assay

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Training Programs

Training Programs

• Introduction to a Cell culture laboratory

• Introduction to laboratory safety – Theory (Biological Safet)

• Bone Marrow MSCs: Theory (Properties, Derivation and Differentiation)

• Primary cultures; Commercial cell lines; Cell thawing; Cell counting, cell, seeding, cell

culture

• Cell imaging; Cell Proliferation; Cell cycle; Cell death

• Media preparation, Cell thawing, Cell counting (Trypan Blue staining), Cell culture

(Adherent cells), Cell imaging (Phase contrast), Cell plating/seeding for in vitro assays

• Introduction to a Cell culture laboratory – II: cGMP laboratory

• Embryonic Stem Cells ( Properties, Derivation and Differentiation)

• Induced pluripotent Stem Cells (Properties, Derivation and Differentiation)

• Cell migration; Cell invasion, Cell migration/Scratch assay, Cell staining and imaging

(Fluorescent), RNA/protein isolation, Assessment of quality and quantity, Primer design-

ing and validation, cDNA synthesis, Gene expression - Real-time PCR demonstration

• Stem Cells in Bone Regeneration (Differentiation into osteocytes),( Histological stain-

ing – Alizarin Red),( Immunohistological staining – Oteopointin, collagen),( Biochemical

assay – Alkaline Phosphatase assay) and (Gene expression assays)

• Stem Cells in Cartilage Regeneration (Differentiation into chondrocytes),( Histological

staining – Toluidine blue, Alcian blue),( Immunohistological staining – Collagen II, SOX9),(

Biochemical assay – Glycosaminoglycan assay),( Gene expression assay)

Course Outline

Fundamentals of cell CultureThe Fundamentals of Cell culture” training program for trainee is designed to cover

comprehensively all the necessary ‘theoretical and practical training’ which are essen-

tial prerequisites for working in a cell culture laboratory. Successful completion of this

training program will enable the student to understand and work independently.

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• Introduction to cytogenetics

• Basic cytogenetic laboratory procedures

Sample processing

Cell culturing

Cell harvesting

Slide preparation

Chromosome banding and staining

• Cytovision karyotyping workstation

• Types of microscopes and its application

• Chromosome numerical abnormalities

• Chromosome structural abnormalities

• Describe banding Nomenclature (ISCN)

• Cytogenetic result, reporting and interpretation

• The basic principle of Fluorescence In Situ Hybrid-

ization in situ Hybridization and their clinical appli-

cations in detecting genetic disorders

Course Outline

APPLICATION OF CLINICAL CYTOGENETICS

• Probe addition and setting up for hybridi-

zation

• Post-hybridization wash and slide viewing

• Computerized image Metasystem advan-

tages, application and Overview

• Nomenclature (ISCN) of FISH result

• Result Interpretation and Reporting using

different types of FISH probe

• Genetic Counselling

Cytogenetic is an exciting, dynamic field of study which analyzes the number and struc-ture of human chromosomes. Changes that affect the number and/or structure of the chro-mosomes can cause problems with growth, development, and how the body functions. Chromosomal abnormalities can happen when egg and sperm cells are being made, dur-ing early fetal development, or after birth in any cell in the body. Changes to chromosome structure can disrupt genes, causing the proteins made from disrupted genes to be missing or faulty. Depending on size, location, and timing, structural changes in chromosomes can lead to birth defects, syndromes or even cancer. However, some chromosomal changes may have no effect on a person’s health. When mutations involve large parts of the chro-mosome such that they are visible under the light microscope, they are called chromo-some aberrations. With routine light microscopy, the smallest visible addition from a chro-mosome is about 4 Mb.

Many cryptic chromosomal rearrangements including micro-deletions, duplications or telomeric rearrangements are often invisible at the routine microscopic resolution.

Fluorescence in situ hybridization (FISH), is a molecular cytogenetic method, where spe-cific fluorescently labelled probes are hybridized to the chromosome spreads of the patient to detect these micro-deletions or duplications. It is also used in confirming cryptic translo-cations and for rapid detection of numerical aberrations. This technique is mostly used as an adjunct to routine karyotyping. It has a wide range of applications in prenatal, postnatal and in cancer diagnosis, and today it has become one of the most essential components of genetic diagnosis.


Training Programs

• An overview on PCR

• Components and Conditions for PCR optimization

• PCR Optimization

• DNA Extraction

• PCR Amplification

• PCR and thermal cycling


• Restriction fragment length polymorphism (RFLP) and its applications

• Restriction enzyme processing of amplified PCR product

• PCR primer designing

• RT-PCR

• UV Transillumination using documentation system and gel interpretation

• Overview of DNA sequencing

• Applications of sequencing

• Isolation of DNA from whole blood

• PCR amplification of DNA using fragment specific PCR primers


• Types of mutations and other applications of genetic analyzer

• Cycle sequencing

• Sequencing data analysis and storage

Course Outline

MOLECULAR GENETICSPCR or polymerase chain reaction is the common tool used for molecular genetic

applications. PCR is carried out for a wide range of applications ranging from gene amplification, mutation screening, and SNP detection. All the advanced techniques in genomics rely on PCR for validation of their outputs before any conclusion could be obtained.

In addition to the PCR applicants will understand how dideoxynucleotides can be used to obtain DNA sequencing. You will learn how sequence reading can be automated using Fluorescent ddNTPs. You will also be able to read the sequence from the gel chromatogram. Moreover, you will learn how to detect the sequence errors and how to apply such high throughput DNA sequence to understanding the human diseases.

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• Basics of Histology & Cytology

• Histology Staining Methods

• Immunohistochemistry (IHC),

• Antibodies: overview, types

• Tissue Microarray (TMA) Technology

• IHC Scoring Systems

• Expression Patterns Profiling & Scoring Systems

• Manual IHC Scoring (light microscope), Subjective method(s) and Objective

method(s)

• Automated: Image Analysis techniques (VIAS)

• IHC validation & applications

• IHC: advantages & limitations

• IHC data analysis (survival, biomarker discovery)

Course Outline

IMMUNOHISTOCHEMISTRY PRINCIPLES & APPLICATIONS OF BIOMARK-ERS DICOVERY

Understanding the molecular causes and progression of human diseases (e.g. cancer, inflammatory bowel diseases, liver cirrhosis etc.) is very useful to biomedical scientists and health care providers to identify and validate targeted biomarkers that help in tai-loring suitable treatment plans for patients. This will in addition help in making informed important for decisions for drug management. Lifestyle changes and quality of life.

One of the main technique used to achieve the above-mentioned goals in quantita-tive pathology is immunohistochemistry (IHC) which allows the characterization of the histopathological features in human diseases and help in the discovery and validation of novel biomarkers (susceptibility, diagnostic, prognostic and/or predictive biomarkers). This advanced hands-on training is tailored to offer the trainees/participants with an up-to-date comprehensive understanding of the IHC technology reinforced by laboratory training and practice.

The technique can be also used to localize a wide range of protein expression in an animal model system.


Training Programs

• Overview on genomics – principal and recent development”

• “The principle of library preparation”

• “Sample preparation”

• Round table

• “NGS applications - Clinical research”

• NGS applications – Targeted sequencing and De Novo sequencing”

• Sequence by Synthesis Technology (SBS) – Library

• “NGS applications – Microbial Genomics”

• Sequencing run metrics and starting a run on MiSeq”

• “Evaluation of the sequencing run“

• “Post-run procedures”

• “Data formats, QC and assembly”

• “Basespace – Introduction to the Illumina cloud-based genomics computing environment

for NGS data management and analysis”

• “BaseSpace – Tools for validation, annotation and visualization”

• “Galaxy – Introduction to a web-based infrastructure for bioinformatics application”

• “Galaxy – Tools for validation, annotation and visualization”

Course Outline

NEXT GENERATIONS SEQUENCING PRINCIPLES AND APPLICA-TIONS IN GENOMIC MEDICINE

Commonly named as the next generation sequencing (NGS) has the power to be the fu-

ture of medical genomics. In this advanced technique, you will understand how to generate

complete sequence information from either whole genome DNA, transcriptome (mRNA) or

microRNA (miRNA) using robotic techniques

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• Principle of microarray technology

• Overview of the gene expression assay workflow on the Affymetrix gene chip system

part1 (cRNA purification)

• Measurement of quantity and quality of nucleic acid

• In Vitro Transcription (Synthesis cRNA)

• cRNA purification.

• Fragmentation of single-stranded cDNA

• Labelling of single-stranded cDNA

• Hybridization to GeneChip

• Priming fluidics station, washing & stain

• Scanning of chip

• Overview of the gene expression assay workflow on the Affymetrix gene chip system,

part II (cDNA purification)

• Bioinformatics upstream analysis

Course Outline

DNA AND RNA MICROARRAY TECHNOLOGIES TECHNOLOGIES: PRINCIPLES AND APPLICATIONS

ThermoFisher/Affymetrix Microarray Gene Chips are used for both scientific researches and for clinical diagnostic applications. Microarray gene expression analysis provides an overview of deregulated pathways and networks in cells and tissue under investigation. Em-phasizes of the program shall be given to the GeneChip Human Gene 1.0 ST Array provides probe sets that comprise more than 750,000 unique 25-mer oligonucleotide features consti-tuting over 28,000 gene-level probe sets for whole-genome gene-level expression studies. The 5 days program provides wet-lab training and demonstration on the ThermoFisher/Affymetrix microarray technology application.


Training Programs

• Overview of Flow Cytometry

• Machine Demonstration (BD FACS Aria III)

• Understanding fluidics

• Understanding fluidics

• Fluorescence & PMTs/Detectors

• Assessing Instrument performance

• Data generation and plotting

• Data analysis

• Multicolor cell surface and intracellular

staining

Course Outline

FLOW CYTOMETRY AND CELL SORTINGFlow Cytometry (FCM), or FACS (fluorescence-activated cell sorting) analysis, is a technol-

ogy that provides swift multiparameter analysis of single cells that have been labelled with

fluorescent probes. Single cells in suspension are passed through a laser beam(s) at rates

ranging from 100-5,000 cells per second using constant pressure. Fluorescence emissions and

light scatter signals are directed by optical dichroic mirrors and filters and collected in pho-

tomultiplier (PMT) photo-detectors and subsequently converted to electronic signals. Besides,

cell sorting requires basic flow cytometry technology with the extra capability to select and

sort cells with specific fluorescence and light scatter properties. Cells selected for sorting are

captured in charged droplets and deflected into collection tubes after entering a high volt-

age field.

Hence, Flow Cytometry is a key technique in single-cell analysis methods extensively used in

life sciences and medicine. In this course, we will cover both the basic theory and the practi-

cal aspects of FACS.

• Multi-color surface/intracellular staining

and analysis

• Fluorescence Spillover and compensation

• Compensation; Fixation for cell cycle

• Cell cycle analysis and Apoptosis assess-

ment

• Cell Cycle and data analysis

• Other applications of flow cytometry

• Mitochondrial membrane potential assess-

ment

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• Introduction to Bioinformatics

• Introduction to Structural Genomics and Proteomics

• Programing in R

• Microarray technology and statistical analysis detecting differentially expressed genes

and altered genome, Genomic integration and visualization of results

• Microarray Data analysis (Partek GS 6.6) and Molecular Pathway analysis (IPA)

• Basics of LINUX Programing

• RT-PCR data analysis

• PyMol, PDB and Protein Structure Visualization

• Application of “R” and “Linux” in data analysis

• Sequence analysis (MEGA tool)

• Molecular Modeling and Docking

• NGS data analysis

Course Outline

BIOINFORMATICS AND DATA MINING

Applicants will understand how to analyze and interpret huge OMICs data sets to con-

clude meaningful interpretation using cutting-edge bioinformatics software and tools.


www.coms.com.sa

King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia

+ 9 6 6 1 2 6 4 0 8 2 2 2 ext . 25973

P.O Box:8021-Jeddah: 1589