Documento que presenta la cartera de servicios y el equipamiento del Servicio Científico Técnico de Secuenciación y Genómica Funcional de la Universidad de Zaragoza y el Instituto Aragonés de Ciencias de la Salud.

1. SEQUENCING AND
FUNCTIONAL GENOMICS UNIT
Biomedical Research Center of Aragón (CIBA)
Zaragoza
Pilar Mozas, PhD

2. SAI UZ
Nucleic Acids
Analysis
UATI IACS
Genomics
Main Services: Real Time-PCR, Sequencing and Genotyping
Study of micro-organisms, plants, animals and humans
Sequencing and Functional Genomics Unit

3. Pre-PCRCloningDNA/RNA Extraction
Post-PCR
Sequencing and Functional Genomics Unit

4. SERVICE EQUIPMENT
DNA extraction
-Manual
-Automated
AutoGenFlex3000 System (Autogen)
Large volume DNA extraction (5 ml)
Whole blood, tissue samples, cultured cells and
saliva
40 samples per batch
KingFisher DuoPrime (ThermoScientific)
Small volume (10-50 µL) or large volume (300-
500 µL)
Interchangeable magnetic rod
6/12/24 samples per run
Analysis of amount and
integrity of Nucleic Acids
Nanodrop-1000 (ThermoScientific)
Qubit 3.0 (ThermoScientific)
Experion Automated Electrophoresis
System (Bio-Rad)
TapeStation 2200 (Agilent)
Projects
Biobank Aragón
Gastrointestinal Pathology (Program to prevent colorectal cancer)
Primary Dyslipidemia
Service Portfolio

5. SERVICE EQUIPMENT
Oligonucleotids design  Oligo 7
 PyroMark Assay Design
Amplification of DNA by PCR  Verity thermocyclers
(Applied Biosystems)
Service Portfolio

6. SERVICE EQUIPMENT
Real Time-PCR:
-Gene Expression analysis
-Genetic Variation analysis:
*SNP genotyping
(allelic discrimination)
*Copy Number Variation (CNV)
-Presence/Absence studies
Real Time PCR instrument:
Viia7 (Applied Biosystems)
Up to 6 fluorophores simultaneously
Medium to high throughput
Interchangeable blocks
- Fast 96-well plates
- 384-well plates
- TaqMan Array Microfluidic Cards
Projects
MicroRNA study in rare diseases
CNV study in pharmagenetics
Service Portfolio

7. SERVICE EQUIPMENT
DNA Sequencing:
-De novo sequencing
-Resequencing
Sequencing instrument:
3500XL Genetic Analyzer (Applied
Biosystems)
Fragment Analysis:
-Microsatellites
-AFLPs
-MLPA
-LOH
SNP genotyping
Service Portfolio

8. Projects
Mutation screening for University Hospitals:
-Hereditary breast and ovary cancer
-Colon cancer
-MODY diabetes
Resequencing to establish the molecular
basis of human hereditary diseases:
-Research on genes related to primary dyslipidemia and
atherosclerosis
-Rare diseases of plasma high-density lipoproteins
-Investigation of the genetics of coronary heart disease risk in
subjects with familial hypercholesterolaemia
-Relationship between chitotriosidase genotype and immune
response to oxidized LDL in subjects with familial
hypercholesterolemia and beta-thalassemia
Service Portfolio

9. Projects
Microsatellite Analysis:
-Characterization of grape vine cultivars by molecular
markers
-Microsatellite fragments size determination for individual
identification and parentage testing, mutation search in
veterinary pathology, mutations involved in ovine prolificacy
species, identification by DNA-barcoding, mitochondrial DNA
biodiversity.
SNaPshot:
-Classification of Tuberculosis Strains.
-Genetic variability in genes related to bone metabolism in
Gaucher Disease patients
Service Portfolio

10. SERVICE EQUIPMENT
NEXT GENERATION
SEQUENCING
Platform Ion Torrent:
PGM
S5XL
Ion Chef
Ion Reporter
Service Portfolio

11. PGM ION S5XL
ION CHEF ION ONE TOUCH 2 ION ONE TOUCH ES
Ion Torrent Platform
ION REPORTER

12. Scalability
Chip 314 316 318 510 520 530 540 550
Reads 0,5 M 3 M 5 M 2-3 M 3-5 M 15-20 M 60-80 M 100-130 M
Output 20 MG 200 MG 1-2 GB 200 MG 1-2 GB 3-5 GB 10-15 GB 25 GB
Ion S5XL Ion GeneStudio S5
Ion GeneStudio S5 Plus / S5 Prime
PGM

13. Projects
WGS
−Whole genome sequencing of samples of Micobacterium Tuberculosis to
compare with the reference genome H37Rv (Ion Xpress™ Plus Fragment
Library Kit, Ion PGM, Ion S5XL).
−Whole genome sequencing of samples of Neisseria GonorNrhoeae to
compare strains.
 Resequencing
−Resequencing of samples of Micobacterium Tuberculosis to compare SNPs
with the reference genome H37Rv by ampliseq panel. (Ion Chef, Ion PGM,
chip 316).
−Identification of the Human Endogenous Retroviruses (HERV-K) over-
expressed in multiple sclerosis by massive sequencing of PCR product (Ion
Xpress Plus Fragment Library kit, Ion S5XL).
 Metagenomics
−Sequencing of the microbiome present in the digestive system of calves (16S
Metagenomics Kit, Ion S5XL, Ion Reporter software).
−Sequencing of the microbiome present in samples of runoff ponds potentially
contaminated with lindane and its isomers. The main interest was the
cyanobacteria and the sphingomonadaceas.
 RNAseq
−Measurement of the expression of genes related to the expansion capacity of
subcutaneous adipose tissue (TAS) by RNAseq in biopsies of TAS (Ion
AmpliSeq™ Transcriptome Human Gene Expression Panel, Ion Chef, Ion
S5XL, chip 540).
Service Portfolio

14. SERVICE EQUIPMENT
Pyrosequencing:
-DNA Methylation studies
-SNP analysis
 Pyrosequencer PSQ
96MA (Biotage)
96 samples simultaneously
Projects
SNP genotyping:
- Photobiology and Dermatology
- Digestive Diseases
DNA methylation:
- Neurosurgery (MGMT promoter methylation in
malignant gliomas)
Service Portfolio

15. SERVICE EQUIPMENT
Mouse Genotyping PCR
Projects
Neurodegeneration:
-Alzheimer
-Amyotrophic lateral sclerosis (ALS)
Service Portfolio
SERVICE EQUIPMENT
Human Cell Line Authentication
by STR profiling
PCR, Sequencer
Projects
Authentication of Diffuse and Intrinsic Glioma of the brainstem protuberance (DIPG) cell lines

16. Service Activity
Solicitudes Importe %
Electroforesis DNA 0 0,00 € 0,00
Extracción DNA 45 8.100,71 € 15,57
Extracción RNA 1 256,50 € 0,49
Cuantificación AN (Nanodrop) 5 13,04 € 0,03
Cuantificación AN (Qubit) 1 17,25 € 0,03
Análisis Integridad RNA (Experion) 4 228,25 € 0,44
Análisis Integridad RNA (TapeStation) 1 14,82 € 0,03
Amplificación AN 0 0,00 € 0,00
Purificación de material PCR 14 78,30 € 0,15
PCR a Tiempo Real (ViiA7) 109 1.914,60 € 3,68
Secuenciación. Análisis completo (3500XL) 79 14.818,96 € 28,48
Secuenciación. Autoanálisis (3500XL) 77 13.826,39 € 26,57
Análisis de Fragmentos ( 3500XL) 18 1.568,85 € 3,02
Pirosecuenciación 13 468,90 € 0,90
NGS 8 10.354,61 € 19,90
Extracción DNA ratones 0 0,00 € 0,00
Genotipado ratones 0 0,00 € 0,00
Otros 25 373,08 € 0,72
TOTAL 400 52.034,26 € 100,00
2018 (Oct 2017-Sept 2018)

17. Service Activity
SECUENCIACIÓN
ANÁLISIS COMPLETO: 28,48 %
(14.818,96€)
SECUENCIACIÓN
AUTOANÁLISIS: 26,57%
(13.826,39€)

18. Service Activity
PCR TIEMPO REAL: 27,25 %
(109 SOL)
SECUENCIACIÓN
ANÁLISIS COMPLETO: 19,75%
(79 SOL)

19. STAFF
Pilar Mozas (pmozas@unizar.es)
Mark Strunk
Irene Santos
Mª José Pueyo
WEBS
http://sai.unizar.es/nucleicos
www.iacs.aragon.es
THANKS!
Sequencing and Functional Genomics Unit