User Manual

Tayside Molecular Genetics User Manual Page 1 of 11
User Manual
East of Scotland Regional Molecular Genetics Service
Human Genetics, Level 6
Ninewells Hospital and Medical School, Dundee DD1 9SY
General Enquiries: 01382 632674
Fax: 01382 496382
Duty Scientist email:- Tay-UHB.moleculargenetics@nhs.net
Head of Laboratory: Dr David Baty (01382 496271 dbaty@nhs.net)
Contact for Clinical Advice Consultant Geneticist: Dr David Goudie
(01382 632035 david.goudie@nhs.net)
Website: http://humangenetics.org.uk/
Laboratory operating hours Monday-Friday 8.30am-5pm
Out of Hours Service is unavailable.
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CONTENTS:
SAMPLE REFERRALS ............................................................................................... 3
SAMPLE TYPES ......................................................................................................... 3
SPECIMEN COLLECTION: ......................................................................................... 3
HIGH RISK SPECIMENS ............................................................................................ 4
SAMPLE TRANSPORT ............................................................................................... 4
SAMPLE STORAGE ................................................................................................... 4
REPORTING GUIDELINES ......................................................................................... 4
LABORATORY REPERTOIRE ................................................................................... 5
SCOTTISH CONSORTIUM REFERRAL LABORATORIES CONTACT DETAILS .. 10
OTHER UK REFERRAL LABS ................................................................................. 10
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Tayside Molecular Genetics User Manual Page 3 of 11
Sample referrals
All samples should be accompanied by a Human Genetics request form, which can be
downloaded from NHS Tayside Intranet either via the Human Genetics website, or from the
Human Genetics section of Clinical Pathways/Information. It is also available on the Human
Genetics Unit website hosted by the University of Dundee.
It is the duty of the clinician/or other health professional to obtain consent from the
patient (or patient’s representative) for genetic testing to be carried out. In submitting a
sample, the clinician confirms that consent has been obtained: (a) for testing and
storage, (b) for the use of this sample and the information generated from it to be shared
with members of the patient’s family and their healthcare professionals (if appropriate).
The following information must be supplied legibly with each sample:
•
•
•
•
Patient's surname and forename
(on sample and form)
Patient's date of birth and gender or CHI
(on sample and form)
Name and address of the healthcare professional requiring report (on form)
Analysis requested and reason for request (on form)
NB: Samples received without 2 unique identifiers on the sample tube will be rejected.
The patient postcode should also be provided as this is necessary for our records and
external invoicing.
If you are sending in a sample from an individual with a known family history please
provide specific details of any known index case and mutation details if available.
Please note that additional forms are required to be completed for some conditions eg breast
and colon cancer, diabetes studies, familial hypercholesterolaemia, HOCM, and long QT
syndrome. Please contact the Dundee Molecular Genetics Laboratory for details. Information
can also be found on Staffnet at:
http://staffnet.tayside.scot.nhs.uk/OurWebsites/HumanGenetics/index.htm
Sample types
Please see section “Laboratory Repertoire” for sample details for each condition. If in doubt,
please contact the laboratory.
NB: Clotted samples are not suitable for DNA/RNA extraction
Specimen Collection:
-
Sample containers must be securely capped after filling
Sample containers must not show visible external contamination by biological materials
Sample containers must be well mixed to prevent clotting. Immediately after collection,
gently invert each blood tube several times to distribute the EDTA throughout the
sample.
Dispose of sharps in a sharps bin after taking a blood sample
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High Risk Specimens
Please note the laboratory does not have the containment facility to handle samples from
individuals with confirmed or suspected prion diseases (eg vCJD) and tuberculosis.
These samples will be discarded by the Laboratory.
Sample transport
Samples sent through the internal mail systems should be placed in sealed plastic bags, with
the accompanying form in a separate compartment and folded to display the lab address
clearly without exposing patient details.
To send blood samples through the post, Royal Mail approved packaging must be used.
This is available from the laboratory on request. All samples should be sent to the address
shown on the front cover of this manual. Samples from NHS Highland are delivered either
by DX Couriers or Royal Mail. Microbiology maintains a generic policy for van transport
(NB141) of samples between PRI and Ninewells, with Genetics and other laboratories as
copyholders.
For optimum DNA/RNA extraction:
• Blood and saliva samples should preferably be received by the laboratory within 3
working days of being taken and stored in the fridge prior to sending.
• Blood samples for BCR-ABL testing should be collected in EDTA and should be received
by the laboratory within 24hrs of sampling.
• Urine samples should preferably be received by the laboratory within 48hrs of sampling.
• Fresh tissue should be sent in appropriate transport media; please contact the laboratory
for information.
Please note that DNA/RNA quality may be affected by delays in transit which may compromise
the testing.
Sample storage
Most DNA/RNA samples will be stored indefinitely unless otherwise requested. Please contact
the laboratory for details.
Please note additional testing may be requested at any time (i.e. no time limit) on stored samples
by contacting the Duty Scientist e-mail account Tay-UHB.moleculargenetics@nhs.net. This is
dependent on the quality/quantity of remaining archived sample.
Reporting guidelines
Written results will be sent to the healthcare professional specified on the request form.
Only in certain circumstances will a report be available via FAX or e-mail (for e-mailing
reports the recipient must have an nhs.net account); please contact the laboratory.
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Tayside Molecular Genetics User Manual Page 5 of 11
Laboratory repertoire
Disorder
Acral peeling skin syndrome;
APSS
Autosomal dominant polycystic
kidney disease; ADPKD
Gene(s)/MutationsTested
TGM5 approx 76% of the
individuals clinically diagnosed
as peeling skin syndrome are
found to carry TGM5 mutations
PKD1/PKD2
Sample
requirement
3ml blood in
EDTA (>1ml
from infants)
TAT
Screen 40
working days
3ml blood in
EDTA (>1ml
from infants)
Screen 40
working days
TGM1 / ALOX12B. Mutations
in TGM1 are detected in
approx 45% of the individuals
diagnosed with lamellar
ichthyosis or non-bullous
ichthyosis
PKHD1
3ml blood in
EDTA (>1ml
from infants)
Screen 40
working days
3ml blood in
EDTA (>1ml
from infants)
Screen 40
working days
Asthma
Β2-adrenergic receptor;
p.Gly16Arg change
20 working
days
Bullous congenital ichthyosiform
erythroderma; BCIE
KRT1 / KRT10
Biotinidase deficiency
BTD
Capillary malformations
RASA1
Cerebral cavernous malformation;
CCM
KRIT1 / CCM2 / CCM3
Detects approx. 75% in familial
cases
CF29v2 kit will detect 29 of the
most common mutations in the
Northern European population
Detects >80% of CF mutations
in Scottish Caucasian
population
Intron 8 polyT test if
appropriate
APC
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA
Screen 40
working days
Tumour
Block>50%
tumour
preferred
40 working
days
Tumour
Block>50%
neoplastic cell
40 working
days
Autosomal recessive congenital
ichythosis; ARCI
Autosomal recessive polycystic
kidney disease; ARPKD
Cystic fibrosis; CF
Colorectal cancer; familial
adenomatous polyposis; FAP
Colorectal cancer – Lynch
syndrome/HNPCC –High Risk
family history
Colorectal cancer-medium risk ?
Lynch syndrome
Colorectal cancer-medium risk ?
Lynch syndrome
MLH1 (MSH2/MSH6
automatically tested in
Edinburgh)
MSI & IHC for MLH1, MSH2,
MSH6 and PMS2. Samples
showing MSI and loss of MLH1
will be screened for the BRAF
p.V600E mutation
MLH1 methylation analysis
under validation for tumour
tissue showing MSI and loss of
Version No. p75.8
Notes
(or at least
100ul of DNA
with conc.
>50ng/ul)
(or at least
100ul of DNA
with conc.
>50ng/ul)
Screen 40
working days
Screen 40
working days
Screen 40
working days
Screen 40
working days
20 working
days
Screen 40
working days
Please provide
details of the
individual’s
ethnic origin
when referring
them for CF
testing.
Tayside Molecular Genetics User Manual Page 6 of 11
MLH1.
Colorectal cancer – MutYH
associated polyposis; MAP
Colorectal cancer/polyps
Colorectal cancer metastatic
MutYH Analysed for 2
common mutations
(p.Tyr179Cys and
p.Gly396Asp). If one mutation
found then full screen
performed
POLE and POLD1 common
mutations
KRAS codons 12, 13 and 61
NRAS codons 12, 13 and 61
BRAF codon 600 if requested
Common trisomies - neonates
T13 / T18 / T21
Common trisomies - prenatals
T13 / T18 / T21
Congenital hypothyroidism
TITF1
Crigler-Najjar syndrome; CN1
/2+UGT1A1 promotor variant
UGT1A1
Deafness – non syndromic
GJB2 sequencing and GJB6
deletions
Deafness –aminoglycoside
related deafness
Mitochondrial mutation
m.1555A>G may be screened
for if evidence of
aminoglycoside use or
maternally inherited
transmission
Dystonia; early onset primary
DYT1
Epidermolysis bullosa simplex;
EBS
KRT5 & KRT14
Epidermolytic Palmoplantar
keratoderma; EPPK
KRT1, KRT9
Ferguson-Smith Syndrome
TGFBR1 mutation screening
Gilbert syndrome
UGT1A1 promoter repeat
Gastrointestinal stromal tumours;
GIST
cKIT / PDGFRA selected
exons / BRAF codon 600
Glomuvenous malformations;
GVM
4 common glomulin mutations
reported to account for 70% of
mutations in GLMN families
HFE; p.Cys282Tyr and
p.His63Asp Approximately
90% of affected individuals are
Haemochromatosis
Version No. p75.8
content
preferred
3ml blood in
EDTA
Screen 40
working days
3ml blood in
EDTA
Tumour
Block>50%
neoplastic cell
content
preferred
>1ml EDTA
from infants
Amniotic fluid or
Chorionic villus
sampling
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
20 working
days
7 working
days
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
Tumour
Block>40%
tumour
preferred
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA **
20 working
days
oncologists
must complete
KRAS referral
form
7 working
days
2 working
days
Screen 40
working days
Screen 40
working days
Screen 20
working days
20 working
days
Screen 40
working days
Screen 40
working days
Screen 40
working days
20 working
days
Screen 40
working days
Biopsies will be
done rapidly on
request
Screen 40
working days
20 working
days
**Mouthwash
samples should
be provided for
Tayside Molecular Genetics User Manual Page 7 of 11
homozygous (carry 2 copies)
for the p.C282Y mutation
Hirschsprung disease
RET
Holoprosencephaly
SHH
Hypo-/hypercalaemic periodic
paralysis
Selected mutations in the
CACNA1S / SCN4A genes
HOKPP1-approx 80% of cases
will have one of the screened
for mutations
HYPP- approx 70% of cases
will have one of the screened
for mutations
CFTR (Intron 8 polyT test if
appropriate) / Y-chromosome
deletions
Infertility / azoospermia / CBAVD
Ichthyosis bullosa of Siemens
(IBS)
KRT2
Ichthyosis vulgaris (IV)
FLG 4 common mutations in
European populations
Loeys-Dietz
TGFBR1 / TGFBR2
Lung cancer
EGFR mutation analysis
Lymphoma
B-cells IGH and IGK
T-cells TCRB and TCRG
FBN1 / TGFBR1 / TGFBR2
Marfan syndrome; MFS
recently
transfused
individuals
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
Screen 40
working days
3ml blood in
EDTA (>1ml
from infants)
20 working
days
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
Tumour
Block>50%
neoplastic cell
content
preferred
Tumour Block or
cut sections
3ml blood in
EDTA (>1ml
from infants)
Screen 40
working days
Screen 40
working days
Screen 40
working days
Screen 40
working days
Screen 40
working days
7 working
days
20 working
days
Screen 40
working days
Medium chain acyl-CoA
dehydrogenase deficiency;
MCADD
ACADM
3ml blood in
EDTA (>1ml
from infants)
Screen 40
working days
Melanoma
cKIT selected exons/ BRAF
common mutations / NRAS
codons 12, 13 and 61
Multiple endocrine neoplasia type
1; MEN1
Menin exons 2-10. In familial
cases where no sequencing
mutation is detected a DNA
sample can be forwarded to
Tumour
Block>50%
neoplastic cell
content
preferred
3ml blood in
EDTA (>1ml
from infants)
BRAF/NRAS
7 working
days/cKIT
Screen 20
working days
Screen 40
working days
Version No. p75.8
Please provide
details of the
individual’s
ethnic origin
when referring
them for CF
testing.
(or at least
100ul of DNA
with conc.
>50ng/ul)
Urgent referrals
will be reported
within 5 working
days for the
common
c.985A>G
mutation.
Tayside Molecular Genetics User Manual Page 8 of 11
Multiple endocrine neoplasia type
2; MEN2
Mitochondrial disorders
Maturity onset diabetes of the
young; (MODY)
Exeter for MLPA
RET selected exons
10,11,13,14,15,16
MtDNA common mutations
causing MELAS, MERRF,
NARP and LHON, & selected
mutations associated with
deafness and/or
cardiomyopathy
HNF1A, HNF4A and GCK
Renal cysts and diabetes
HNF1B
Myeloproliferative neoplasms;
MPN
Myotonic dystrophy (DM1)
JAK2; p.Val617Phe / then
JAK2 exon 12 / CALR exon 9
/ MPL exon 10 reflex testing as
appropriate
CAG repeat length
Neurofibromatosis type 1; NF1
NF1 screen
Occulopharyngeal muscular
dystrophy; OPMD
PABPN1 repeat
Pachyonychia congenita Types I
and II
Hot-spots of the KRT6A,
KRT6B, KRT6C, KRT16 and
KRT17 genes
PARK2 / LRRK2 / PINK1
Sequence analysis of PARK2
gene plus MLPA analysis for
deletions of PARK1, PARK2,
PARK5, PARK6, PARK7,
PARK8 and ATP13A2 genes
(kit can also detect LRRK2
p.Gly2019Ser mutation)
Parkinson disease
Pendred syndrome
SLC26A4 / FOXI1
Phaeochromocytoma /
Paraganglioma
SDHB / SDHC / SDHD;
TMEM127 / MEN2 / VHL /
MAX
PLP / GJA12. 50-60% of
cases have a duplication of the
PLP gene 30% of remaining
cases have a point mutation
EXOSC3 – common mutation
only
Pelizaeus-Merzbacher disease;
PMD
Pontocerebellar hypoplasia type1
Palmoplantar keratoderma; PPK
K1, K5, K9, K10
Proximal symphalangism
GDF5 / NOG1
Version No. p75.8
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
Screen 40
working days
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
Screen 40
working days
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
20 working
days
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
20 working
days
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
Screen 40
working days
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
20 working
days
20 working
days
Urine sample for
adult patients
esp. if MELAS
indicated. Must
reach lab within
48 hours
Screen 40
working days
20 working
days
Screen 40
working days
(or at least
100ul of DNA
with conc.
>50ng/ul)
Screen 40
working days
Screen 40
working days
Screen 40
working days
Screen 40
working days
Screen 40
working days
Screen 40
working days
Referrals
accepted from
neurology only
Tayside Molecular Genetics User Manual Page 9 of 11
Thoracic aortic aneurysm and
dissection (TAAD)
ACTA2
Thrombophilia
p.Arg506Gln / g.20210G>A
Tuberous sclerosis
TSC1 and TSC2
Von Hippel Lindau; VHL
VHL
Version No. p75.8
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
3ml blood in
EDTA (>1ml
from infants)
Screen 40
working days
20 working
days
Screen 40
working days
Screen 40
working days
Tayside Molecular Genetics User Manual Page 10 of 11
Scottish Consortium Referral Laboratories Contact Details
North of Scotland Regional Genetics Service
Polwarth Building,
University of Aberdeen
Medical School,
Foresterhill,
Aberdeen
AB25 2ZD
Phone 01224 553893 E-mail grampian.molgen@nhs.net
South East Scotland Genetics Service
Molecular Medicine Centre
Western General Hospital
Crewe Road
Edinburgh
EH4 2XU
Phone 0131 651 1116 / 1270 E-mail edinburgh.dna@luht.scot.nhs.uk
West of Scotland Genetics Service
Laboratory Genetics
Level 2B
Laboratory Medicine
Southern General Hospital
Glasgow
G514TF
Phone 0141 354 9330 E-mail gg-uhb.geneticsglasgow@nhs.net
Other UK Referral Labs
The referral labs which we use most regularly send samples for testing include:
Birmingham:
West Midlands Regional Genetics Laboratory
DNA laboratory
Birmingham Women’s foundation Trust
Birmingham
B15 2TG
0121 627 2710 genetics.lab@bwhct.nhs.uk
Cardiff:
All Wales Molecular Genetics Service
Institute of Medical Genetics
University Hospital of Wales
Heath Park
Cardiff
CF14 4XW
029 2074 2641 michaela.john@wales.nhs.uk
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Tayside Molecular Genetics User Manual Page 11 of 11
Guy’s London:
Vipath
Genetics Laboratories
5th Floor, Tower Wing
Guy’s Hospital, Great Maze Pond
London
SE1 9RT
020 7188 1696/2582 David.Ellis@viapath.co.uk
Manchester:
Regional Genetics Laboratory Services
Genetic Medicine
6th Floor, St Mary’s Hospital
Oxford Road
Manchester
M13 9WL
0161 276 6122
Sheffield:
Sheffield Diagnostic Genetics Service
Sheffield Children’s NHS Foundation Trust
Western Bank
Sheffield
S10 2TH
0114 2717003 SDGS@sch.nhs.uk
Addresses / Contact details of other UK laboratories
Addresses / Contact details of other UK laboratories which we refer samples to
can be obtained by contacting us directly, or follow this link to the UKGTN
home page where you can search for test and laboratories:
http://www.ukgtn.nhs.uk
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