biochemistry 101
TRANSCRIPT
Biochemistry for Software Developers
Important Disclaimer This presentation is intended for IT use
only and is intended as background information only. It is not a substitute for speaking with a qualified clinician, which you should do if you have a question on biochemistry fundamentals.
Objectives
Introduction to biochemistry Biochemistry techniques Prenatal diagnosis Common genetic abnormalities
Key Biochem Personnel Senior Director = Dr. Phil Wyatt, M.D. Directors = Faye Myrick, Stan
Marenberg, Deirdre Thomas Lab Manager = Nancy Maner Senior Techs = Doris Langley, Kim
Pritchard Arielle Mills
Santa Fe Development SMEs Biochemistry = Jim Walters, Joe Francis
Jim specializes in legacy, especially gzuBIO and Modeling. Jim is on the BSA team now, but is still an SME
Joe specializes in new apps, especially AutoApp, Review, and Upload
Biochemistry requires a team effort Accessioning = Hemanth Kumar (TCS),
Robert Bradford (on security team now) Reporting = Jose George
Santa Fe Development Staff Biochem is 75% of our business Development staff = Joe Francis and Gary Topp Biochem Project Manager = Mary Sorvig Three QA staff know biochem well
Carlos Guevara, Vickie Sievers, Ram Turaga Training Indira Varanasi and Vanita Patel
TCS personnel onsite do customer service Srini Srikiram, Triven Mukkala
Analysts (Focused on GeDI) Juan Blea, Tracy Archuleta, Regina Garrick, Jim
Walters, Jeannie Bilbo
Prenatal Genetic Concerns 46 chromosomes in 23 pairs
Some people have an extra chromosome, a “trisomy”
Downs Syndrome (T21) T18 (Edwards Syndrome) Neural Tube Defects (Spina Bifida
mainly) T13 is common, but is a FISH test
Genetic Disorder Screening Only Healthy pregnant women typically get
four sets of labs Test happen only when indicated
First prenatal visit Pregnancy test, Pap smear, Blood type and
Rh type, Antibody screen, HCT/HGB (CBC), Rubella, VDRL, Urine, HBsAg, HIV
GG handles the second set of labs Unrelated set of labs in eight month Unrelated set of labs in ninth month
Who Should be Screened? Women over 35 Women with a history of problem
pregnancies Women with medical problems like high
blood pressure, diabetes, asthma, or epilepsy
Women whose families (or partner’s families) have a history of genetic disorders
Twins (or more) Women who have had miscarriages
When Does Screening Take Place? Late in first trimester at 10.4 weeks to
13.9 week gestational age Optimally 10-12 weeks
Second trimester at 14.0 weeks to 21.9 weeks gestational age Optimally 16-18 weeks
Robert and His Family
Trisomy 21 Karyotype
Trisomy 21 = Down’s Syndrome
Results in Down syndrome 1 in 800 liveborn infants ~75% spontaneously abort Phenotypic features
“Dysmorphic” features Mental retardation Low muscle tone Congenital heart disease Gastrointestinal anomalies
Trisomy 18
1 in 10,000 liveborn infants ~95% spontaneously abort Characteristic features
Small for gestational age Characteristic hand posturing
with overlapping fingers Small face and chin Rocker-bottom feet
Trisomy 18
Trisomy 18
Neural Tube Defects Open spina bifida (OSB)
Latin for “split spine” Is the spinal cord closed?
Other NTD conditions involve non-fusion of brain and are worse.
Screening vs. Diagnosis Our biochemistry tests cannot diagnose a
genetic condition That is where cyto comes in if needed
Biochemistry tests do suggest the likelihood of a genetic condition There will be some false positives and false negatives
General Process Physician orders a non-invasive test If non-invasive test suggests risk, Amniocentesis is
typically ordered along with chromosome analysis, which will diagnose a problem
Other tests are 80-90% accurate; amnios are 99% accurate
Genetic Counseling is the last stage
Genetic Counseling We have counselors that travel the
country, often with bad news… Must be board certified in genetic
counseling Also serve as SMEs internally Work closely with Client Services
Analytes hCG: Human Chorionic Gonadotropin PAPP-A: Pregnancy-associated plasma protein A
Low level indicates Down’s AFP: Alpha-fetoprotein
Produced by the fetus and mainly goes away a year after birth
High level indicates NTD, low level indicates Down’s UE3: Unconjugated Estriol
One of three main estrogens Low level is indicative of Down’s, T18
DIA: Dimeric Inhibin A High level is indicative of Down’s
Specimen Types Serum (Blood) Amniotic Fluid Dried Bloodspot Occasional Outliers like cystic hygroma
Five Lab Flows One-shot serum (blood) tests
FIRSTSCREEN: Uses NT as well MSAFP = Maternal serum AFP AFP3 = Three marker test AFP4 = Four marker test
Amnio: One-shot amniotic fluid tests AFAFP = Amniotic Fluid AFP
Integrated and Sequential INT-1/INT-2 SEQ-1/SEQ-2
Tay Sachs LSD
Tests Ordered in 2008 as of 10/5/08 817247 total 75378 Sequentials 71885 AFP4 55232 FIRSTSCREEN 44521 AFAFP 32309 Integrateds 15216 MSAFP 3689 AFP3
Integrated and Sequential Tests Test late in first trimester and early in
second trimester Integrated reports only after result of
second serum Sequential reports on 1st trimester
results, then again in 2nd trimester “Full Integrated” adds non-chemistry
markers Not separated at database level “302
issue”
IT Issues Around INT and SEQ Linking
What if two different patients are used for these procedures
PTRF/PTRF Reminder Need to remind clients to call patients to
come in for the second part of the test
Tests and Analytes
Test AFP HCG UE3 DIA PAPP-A
FIRSTSCREEN
X X
SEQ-1 X X
INT-1 X X
Test AFP HCG UE3 DIA PAPP-A
AFAFP X
AFP3 X X X
AFP4 X X X X
MSAFP X
SEQ-2 X X X X X
INT-2 X X X X
Multiple of the Median (MoM) How far does an individual test result
deviate from the median? Need results from several hundred
women at each GA to establish a set of medians
Used for a variety of medical screening tests where the medians are highly variable
Medians are sometimes updated
Multiple of the Median (MoM) Experienced personnel can simply look
at the MoMs and visualize the risks Simple math: Divide the chemistry test
result by the median for that population; it will ideally come out to 1.0 and should not deviate much from 1.0
Weight correction factors We truncate the weight at high and low
weights (90 and 280 lbs?) for calculation purposes, but not for reporting purposes
MoM Adjustments Twins
Hard limits on triplets and no risk assessment available at all for higher parity
Ethnic Origin “Native” Japanese African-American Other distinctions could be made
Insulin-dependent diabetes (IDDM)
Risks and the Math Behind Them It’s all about statistics and accumulated
experience Calculate the MoM from the raw chemistry values Use the MoMs to calculate the risk Moderately complex mathematics
Logarithmic equations Calculator project to refine/redefine what we are doing
Gestational Age: How many days/weeks since conception? Weeks GA used to drive the calculation coefficient “GA Methods” include Ultrasound, CRL measurement,
and Last Menstrual Period (LMP)
Risk Adjustments Anti-Convulsant meds (for epilepsy
patients) Egg Donors
Amniocentesis
Amniotic fluid provides a sterile environment and cushion for unborn baby
14 – 21 Weeks Gestation (most at ~16 weeks with ~30cc fluid)
Early amnios done at 12 weeks (little fluid) Fluid contains skin cells/gut cells from baby Chorionic Villus Sampling
Takes a piece of the placenta Can be done in first trimester, but is more risky
Amniocentesis Advantages
Testing fetus directly rather than indirectly through expectant mother
Can test for neural tube defects – increased alpha-fetoprotein in amniotic fluid indicates a 90% chance of a neural tube defect
Disadvantages Later in pregnancy 1/2% chance of pregnancy loss due to the
procedure (miscarriage, bleeding, infection)
Amniocentesis Ultrasound always done before the Amnio CHROM test (cyto analysis) almost always
ordered with Amnio Separated cells must be cultured in cyto lab
to have enough for analysis No culturing necessary for biochemistry
screening tests AChE (Acetylcholinesterase) test often
added Depends on how Amnio results are looking…
HGB
Amniocentesis
Processing Amniotic Fluid
Genetic Disorder Risk Factors Family History Maternal Weight Maternal Age
Age of an egg donor also applies
Mother’s age
Risk for having a child with Down syndrome
20 1 in 1,60025 1 in 1,30030 1 in 1,00035 1 in 365 40 1 in 90 45 1 in 30
Fetal Measurements The role of sonographers
There are differences among them Nuchal Translucency (NT)
At 11-13 weeks, measure the amount of fluid behind the baby’s neck
Crown-to-Rump Length (CRL) How big is the baby from top of head to
buttocks? This measurement drives calculation of
gestational age
Tay Sachs A lysosomal storage disease Children develop normally, but slowly
deterioriate and die by the age of five Cherry red spot in each eye Not a part of mainstream biochemistry
Different codebase Enzyme test and DNA test
Tay Sachs New Directions Robots, Robots, Robots
Working with the R&D Lab Dr. Deirdre Thomas is the expert New Assay Under Development
New software, new equipment “Tay Sachs Automation” is biggest Santa
Fe development project at the moment Tied to AJ Panel Not a whole lot shared from an
architecture pipeline perspective
Lysosomal Storage Diseases Due to lacking enzymes that break down
bad things; “fatty build up” Gauchers, Niemann-Pick, 40 others… Biochem team wants to integrate into
LMS, but we have a separate application for now
Smallest line, no concrete plans for now Jim Walters is the IT SME
Biochem Lab Process
A Quick Taste of Biochem IT Systems Biochem Core Pipeline Architecture Biochem LMS Integration Biochem Peripheral Applications Modeling Reporting
Biochem Core Pipeline Architecture
DSX (INHIBIN)
DXI (T2 AFP, hCG, UE3)
DPC (T1 hCG, PAPP-A)
Run Creation
Result Tables
B_ASSAY_RESULTSB_AF_RESULT
B_SERUM_RESULTSB_INTEGRATED_RESULT
Analyzer/Verify(VB6)
Supervisor Review(WPF
Application)
Check Run Creation Results
Senior Tech Pulls Data; Check for
Problems and Trends
Analyze Run Data
Review Specimens
Auto-Recalc(WCF
Service)
Case Calculations and Risk
Interpretations
Upload
Upload (WPF
Application)
Modeling(gzuBIO –
VB 6)
Auto-Approval
Manual Approval
Auto-Approval(WCF Service)
gzRep32 (VB6) and REP.EXE
(VB3)
Director Review
REPORTED
Accessioning Tables
AC_SPECIMENAC_SPECIMEN_PROCEDURE
AC_FILEAC_CASE
AC_GEST_AGEAC_PATIENT
AC_RACEAC_RELATIONSHIP
Reporting Tables
Get Sample Data
REP_AFACHEREP_FIRSTSCREEN
REP_INTSCREENREP_AFP3REP_AFP4
REP_MSAFP
Biochem LMS Integration
Samples
Amniotic Fluids
Blood
Dried Bloodspot
Report Distribution
Remote Station (VB 6)
Faxing
Autofax
Rightfax
Accessioning
ACC (VB6) Accessioning Tables
AC_SPECIMENAC_SPECIMEN_PROCEDURE
AC_FILEAC_CASE
AC_GEST_AGEAC_PATIENT
AC_RACEAC_RELATIONSHIP
OTHER
Event Recording
Audit Systems
Problem Track
Common Systems
Data Portal
Exception Handling
Entities
Common Components
Security
Notification
Biochemistry Core System
ECI Systems
Accessioning Processes
Biochem Peripheral Applications PTRF, PTRF Reminder, gzLink, gzMedians Cancel/Convert, ICIS, gzuDeUnite Call Tracker, gzuMaintain, gzuMRPro Nontech, LSD, Bluesheets, Requeue gzuBIODSX_SF and instrument interface
apps
Modeling Part of gzuBIO If you want to understand biochemistry, start
here If you are a biochem developer and do not use
modeling, you aren’t really a biochem developer yet
If you do something new and do not match modeling, your stuff is probably broken
Nonetheless, modeling is complex enough that we find some new issue every week or two
Jim Walters is the SME
Modeling
Reporting IMPORTANT to distinguish between
reporting a result through a biochem director and physically sending the reports through large reporting support team
Three types of reports: Positive, Negative, Inconclusive Positive is bad, negative is good, Inconclusive
usually because missing some data HOLD-ACC with Client Services Followup
Reporting Interpretations based on fragments Most of our reports go out automatically
This includes positives and negatives, but not inconclusives
Getting “director review” to zero is a lucrative goal
Manual Reporting split across REP.EXE and gzRep32
Report Curve
Reporting: Director Review Data Flow
Upload
Recalc
Modeling Auto-Approval
Reported
DIRREV
Cyto and FISH
Diagnose genetic disorders rather than just predict them
Cyto = inspection of karyotypes
FISH = Fluorescence in situ hybridization
FISH uses DNA technology applied to chromosomes
FISH provides higher resolution answers than standard cyto FISH is like like a zoom lens
LOTS of cyto directors
1321
18XY
Down’s Syndrome (Male)
1321
18XY
Trisomy 18 (Male)
Molecular Genetics: FISH
rRNA15cen