Practical Genetic Counseling For The Laboratory - (8. Genetic Counselor Role in Laboratory Case Management)

8
Genetic Counselor Role in Laboratory Case

Management
JESSICA R. BALCOM, ANNE M. BANDHOLZ, AND AMY L. SWANSON
Since the completion of the Human Genome Project in 2003, the number of clini-
cally available genetic tests has climbed rapidly from a few hundred to over 27,000
tests (National Center for Biotechnology Information n.d.) and the percentage of
genetic counselors reporting that they work in a diagnostic laboratory-based role
has more than doubled from 2004 to today (Parrott and Manley 2004; National
Society of Genetic Counselors 2016). The increasing presence of genetic counselors
in a laboratory-based setting has likely resulted not only from the growing number
of available genetic tests but also from the level of complexity involved with testing
strategies and interpretation of results as well as the importance of effective results
communication. Laboratory-based genetic counselors (LBGCs) are a valuable resource
to medical genetics specialists (medical geneticists and clinical genetic counselors) as
well as healthcare providers who do not specialize in genetics. A 2003 survey of clinical
genetic counselors found that, even with their high-level understanding of the intrica-
cies of the genetic testing process, greater than 50% relied on laboratory personnel
for assistance with various aspects of the testing process (McGovern et al. 2003). And
Copyright © 2017. Oxford University Press, Incorporated. All rights reserved.
assessments of nongenetic providers have identified lack of comfort with and under-
standing of genetic testing (Suther and Goodson 2003; Klitzman et al. 2013; Mikat-
Stevens et al. 2015). One such publication involving a survey of internists found that
70% of respondents felt they needed more training on when to order tests, 77.3%
needed more training on how to interpret results, and 82% needed more training on
how to counsel patients (Klitzman et al. 2013). While a multipronged approach is
required to meet the identified training needs of nongenetic providers, LBGCs are one
way in which these providers can receive assistance with the ordering and interpreta-
tion of genetic testing.
LBGCs have a wide range of roles and responsibilities (McGovern et al. 2003;
Scacheri et al. 2008; Christian et al. 2012; Zetzsche et al. 2013; Waltman et al. 2016),
depending in part on the educational background/expertise of other laboratory
staff, the types of testing offered, and any state regulations related to competencies
of staff performing various aspects of the testing process. For example, in a labora-
tory with limited devoted billing and marketing experts, LBGCs may be called upon
to apply their background and expertise to these areas. The genetic counselor’s skill
207
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2017. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/cityuhk/detail.action?docID=4828920.
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208 P ractical Genetic Counseling for the L aboratory
set is versatile, and counselors in laboratory-based roles have reported job duties
ranging from involvement in result interpretation and reporting, to marketing and
website design, to client and staff education (McGovern et al. 2003; Scacheri et al.
2008; Christian et al. 2012; Zetzsche et al. 2013; Waltman et al. 2016). Several stud-
ies (Christian et al. 2012; Waltman et al. 2016) have shown the most frequently per-
formed roles for LBGCs are customer liaison/case coordination and interpretation/
result reporting, but laboratory type (e.g., molecular, cytogenetic, newborn screening)
does seem to influence the responsibilities of LBGCs. For example, in Waltman et al.’s
study, LBGCs working in cytogenetic laboratories reported more frequent involve-
ment with specimen handling issues, while LBGCs in cell-free fetal DNA testing labo-
ratories reported the highest rate of involvement with sales and marketing (Waltman
et al. 2016). For all LBGCs, accredited genetic counseling training programs prepare
counselors for laboratory-based roles by providing foundational knowledge and skills
consistent with the American Board of Genetic Counseling’s practice-based compe-
tencies (American Board of Genetic Counseling 2010).
This chapter focuses on the case management roles of LBGCs throughout the
stages of genetic testing, including pre-analytic (communicating with clinicians prior
to sample submission, test utilization management within the referral laboratory,
identification of potential testing barriers upon sample receipt), analytic (communi-
cation of test delays), and post-analytic (assisting with results interpretation, drafting
of report language, and contacting clinicians with results and for long-term follow-up)
(Fig. 8.1). The themes of LBGCs as client liaisons and patient advocates are empha-
sized throughout the chapter.
Pre-analytic Stage
CO M M U N I C AT I O N A N D CO O R D I N AT I O N P R I O R
TO SAMPLE SUBMISSION
As liaisons between laboratory personnel and external clients, genetic counselors in

reference laboratories are well positioned to manage case coordination and communi-
cate with healthcare providers and client laboratories regarding test utilization. In this
sense, the LBGC’s role in case management may begin even before a patient is evalu-
ated in the clinic or a specimen is received in the laboratory for testing if the clinician
contacts the lab with questions. Pretest communication with LBGCs helps the clini-
cian navigate expanding genetic test menus and also provides the opportunity for the
lab to obtain information and establish expectations between the laboratory and the
clinician, who in turn relays these expectations to the patient (Scacheri et al. 2008).
The types of questions often asked by a clinician prior to sending a specimen to a
laboratory include questions about assay sensitivity and specificity, specimen require-
ments, turnaround time, costs, and the testing methodologies used (McGovern et al.
2003). This pretest communication also provides the LBGC an opportunity to discuss
test limitations and appropriate testing strategies, including identification of the most
relevant family members to test, and prepare the clinician for potential test outcomes.
Such dialogue facilitates the informed consent process by empowering the clinician
Pre-analytic Analytic Post-analytic
Prior to Sample Receipt

Communicate with clinician to assist with:
Client Communication Interpretation of Test Results
• Test menu navigation Communicate with clinician regarding:
• Delayed turnaround time Integration of clinical information with
• Obtaining relevant information for lab test result(s), including:
• Test failures
• Establishment of expectations for clinician, • Review of indication for testing
• Discrepant results
lab and patient • Determining clinical significance of
Coordination of testing for: results
• High complexity and/or time-sensitive • Accurate risk revision
cases • Identification of potential testing errors
• Unusual/unvalidated specimens • Follow-up testing recommendations
• Non-routine testing requests
Upon Sample Receipt

Review of sample information Reporting of Test Results
• Communicate anticipated delays or new sample • Drafting report verbiage
requests with the clinician • Calling clinician with test results
Review for appropriate test utilization and barriers to
testing via:
• Patient demographics
• Clinical information, prior test results, and family
history information
• Specimen type
• Indication for testing
• Confirmation of Compliance with lab, state, and
federal requirements
Throughout all stages of genetic testing, LBGCs assist with: sample triage decisions, internal test coordination, and coordination of sendout testing
Figure 8.1 LBGC involvement across the stages of genetic testing.

with information to support the testing discussion with the patient and allows the
early identification and resolution of potential barriers to the testing plan.
Pretest communication is particularly important in the context of complex or
high-priority test requests. This may include cases that require specimen sharing for
sendout testing or special requests for time-sensitive testing, testing on unusual or
unvalidated specimen types, or requests for a deviation from the typical testing algo-
rithm (e.g., request for nonroutine reflex testing). The complexity of these requests
makes them more prone to complications and testing delays, and because of this, labo-
ratories may set explicit recommendations or requirements for clinicians to contact
the laboratory prior to sending such specimens.
Early communication allows the LBGC to obtain the necessary details of the case
to facilitate tracking and ensure that testing proceeds without delays (Scacheri et al.
2008). This includes the patient name and date of birth, specimen(s) to be sent for
testing, test(s) to be performed, and clinician contact information. Also, as discussed
above, advance notification of special requests allows the LBGC to assess the feasibil-
ity of the request, review any relevant limitations of testing with the clinician, and
discuss expectations for the testing process (e.g., whether turnaround time, reporting
format, or other testing parameters will be affected by the special request).
R E V I E W O F S A M P L E I N F O R M AT I O N A N D S E N D O U T T E S T
C O O R D I N AT I O N
Once a specimen arrives in the laboratory, coordination is key to ensure timeliness
of testing and fulfillment of clinician expectations for complex or high-priority test
requests. Genetic counselors can facilitate communication among laboratory person-
nel, such as laboratory technicians and sendout test coordinators. For instance, the
LBGC may communicate with laboratory personnel to ensure sufficient sample is
dedicated to the various tests requested, or to facilitate expedited processing for time-
sensitive cases in order to accommodate turnaround time expectations.
Problematic samples are often identified upon arrival and may warrant communi-
cation with the clinician before testing begins. In some instances, the specimen sub-
mitted may be an inappropriate or unvalidated sample type or may be of insufficient
quantity or quality to attempt testing. In other circumstances, the laboratory may
be willing to attempt testing on specimens that do not meet minimum quantity or
quality requirements. In either case, the LBGC may contact the clinician to request a
new specimen or, if testing will be attempted, caution the clinician regarding the pos-
sibility for test failure or delays (Scacheri et al. 2008). Sample issues resulting in test-
ing delays may occur with any sample type but are particularly common for prenatal
samples, where the amount of specimen available is limited and cell culture expansion
may be required to obtain sufficient sample to initiate testing. Upfront communica-
tion regarding such issues enables the clinician to prepare the patient for potential
outcomes and complications.
In some cases, the specimen is limited and an additional sample is not readily
available (e.g., patient is deceased, or for prenatal cases where additional sample can
be obtained only via an invasive procedure). The LBGC may assist with coordination
C a s e M a n a ge m e n t 211
of sendout testing if multiple assays must be performed on such limited specimens.

Sendout testing coordination from the hospital laboratory setting is discussed in
detail in Chapter 10, “Genetic Counselor Role in Hospital Test Utilization.” However,
genetic counselors in the reference laboratory setting also participate in sendout test-
ing coordination, working closely with the clinician, the receiving laboratory, and
internal lab personnel to coordinate prudent sample allocation, balancing the need
for results for each test desired. In some cases, the LBGC may need to provide support
and guidance to clinicians if inappropriate sendout testing is requested. Depending on
reference laboratory policy and services, the reference LBGC may also need to clarify
with the clinician and the receiving laboratory which party is responsible for billing,
paperwork, and shipping logistics. Sendout testing coordination may be ongoing
throughout the testing process, especially in the post-analytic phase, when any send-
out testing ordered in a reflex fashion is arranged (Fig. 8.1).
T E S T U T I L I Z AT I O N M A N A G E M E N T A N D I D E N T I F Y I N G
BARRIERS TO TESTING
The majority of samples received in the laboratory will arrive without prior com-
munication with the clinician. Thus, any potential barriers to the clinician’s test-
ing plan and appropriate testing strategies will not have been addressed prior to
sample receipt. With the increasing number of genetic tests being ordered, many
of which are processed by local laboratory sendout staff, there is a significant
risk for incomplete requisition forms and improper ordering of genetic testing
(Wain et al. 2012). As such, many testing laboratories employ genetic counselors
to review incoming cases for appropriate testing. The vigilant review of genetic
test orders by LBGCs directly benefits patients, medical institutions, and insurers
because incorrectly ordered testing increases healthcare costs and can affect medi-
cal decision making (Dickerson et al. 2014; Kotzer et al. 2014; Miller et al. 2014).
Genetic testing can be uniquely expensive and may not be reimbursed by insur-
ance (Dickerson et al. 2014; Kotzer et al. 2014; Miller et al. 2014). Thus, pursuing
genetic testing that is most effective for the differential diagnosis is imperative to
the prudent use of resources.
Beyond cost considerations, other significant risks may result from unneces-
sary or inappropriately ordered genetic testing. Results from an inappropriate test
could provide a significant misdirection in the patient’s diagnostic odyssey, where a
“normal” result could lead to the misperception of ruling out the disorder in ques-
tion. Ultimately, this can create false reassurance for the patient or family, inaccu-
rate genetic counseling, and an erroneous understanding of recurrence risk (Kotzer
et al. 2014). Results from unnecessary or inappropriate testing may reveal incidental
findings or results of uncertain significance, which complicate counseling and may
cause patients anxiety or emotional distress (McGillivray et al. 2012; Reiff et al. 2012;
Bowdin et al. 2014). For instance, if full gene sequencing is ordered instead of a tar-
geted assay for a known familial mutation, a variant of uncertain significance in a
different area of the gene than the familial mutation may be revealed that would not
have otherwise been detected if a targeted assay had been ordered.
Figure 8.2 LBGC test utilization review checklist. *This checklist is meant to serve
as a guide to assist LBGCs with completing a review of necessary items upon sample
receipt. Some criteria may not be relevant depending on the laboratory, test menu, and
case details.
Brierley et al. describes several poignant case examples in the context of test misor-
ders for heritable cancer syndromes resulting in false reassurance and inaccurate med-
ical management recommendations (Brierley et al. 2012). Scacheri et al. also presents
case studies that demonstrate the potential impact to patient care and management
if insufficient or incomplete information is received by the laboratory and the genetic
counselor’s role in resolving or preventing these circumstances (Scacheri et al. 2008).
Such instances are a liability issue for both the clinician and the laboratory. Litigation
has demonstrated that the laboratory itself may be liable if the information submit-
ted with the test order suggests that the testing requested is either not appropriate or
may not be sufficient to answer the diagnostic question and the laboratory does not
attempt to resolve the issue (Wuth v. Lab. Corp. of America).
The LBGC reviewing test orders must also assess for evidence of a gap between
what the clinician is expecting testing to provide and what testing will actually deliver,
along with other barriers to the clinician’s testing strategy. The presence of an expec-
tation gap does not necessarily mean that the test ordered is incorrect; rather, it
presents an opportunity for the genetic counselor to assess the clinician’s awareness
about the benefits and limitations of the testing and to respectfully supply informa-
tion beneficial for patient care and a positive clinician experience. For instance, some
conditions with multiple genetic etiologies require several tests to exclude a diagnosis.
If the chosen test evaluates an uncommon etiology, it is not an effective first-tier test
if testing with a higher diagnostic yield is available. For example, if CDKN1C gene
sequencing was ordered as the initial test for a patient with a suspected diagnosis
of Beckwith-Wiedemann syndrome, the LBGC may recommend changing testing to
methylation-based analysis of the 11p15 imprinting regions, since methylation analy-
sis would have an expected diagnostic yield of up to 85% compared to only 5% to
10% for CDKN1C gene sequencing (Choufani et al. 2010). Moreover, expectation gaps
can have an impact on the informed consent process. Misconceptions on the part of
the clinician may result in inaccurate information presented to the patient in pre-
test counseling or the lack of discussion regarding possible outcomes (Scacheri et al.
2008). This in turn may contribute to difficult posttest counseling and unexpected
results for the patient. Essentially, expectation gaps create educational opportunities
that are case-specific but can serve the clinician in similar situations in the future.
The following information and examples provide guidance on the various elements
of test order review and how these details are used to (1) evaluate if ordered testing
is appropriate, (2) assess for expectation gaps, and (3) identify barriers to the desired
testing strategy.
Review of the Requisition Form

The LBGC’s training and experience are applied to the thorough review of requisition
forms and any additional documentation submitted with the specimen. The LBGC
must review all details in order to understand the context of the case and identify
potential concerns. A sample checklist of items for the LBGC to assess for appropriate
test utilization is provided in Figure 8.2. Depending on the laboratory’s test menu,
additional items may be worthy of consideration, while others may be less relevant.
Demographic information, sample information, and indication for testing should all
be compared to the testing requested. In addition, all documented conversations with
the clinician regarding the testing plan prior to sample submission must be reviewed.
When necessary, the LBGC may need to contact the clinician for additional details or
missing information in order to complete his or her assessment.
Review of basic demographic information can reveal duplicate testing, which is
commonly encountered by most laboratories. Test orders can be inadvertently dupli-
cated when the patient’s care has been transferred to a new physician or when multiple
specialists are participating in the care of the patient. For molecular, cytogenetic, and
some biochemical genetic testing for congenital conditions, repeat testing is typically
without benefit (Kotzer et al. 2014) unless significant changes to methodology or test
design result in improved detection rates compared to the previously completed assay.
If there is no benefit to repeat testing, or if the benefit is marginal, discussion with the
clinician prior to test initiation is indicated. In many cases, the LBGC can coordinate
the release of the relevant report to the treating clinician while maintaining Health
Insurance Portability and Accountability Act (HIPAA) compliance (U.S. Department
of Health & Human Services n.d.).
Some additional examples pertaining to the importance of requisition form review
in the context of test utilization assessment are in Box 8.1.
Review of Prior Test Results, Family History, and Clinical Notes

In addition to the test requisition form, useful information can be obtained from
other documentation that may be submitted with the sample, including prior test
results, clinic notes, and pedigrees (Box 8.2). In some cases clinicians may provide
very limited information on the test requisition, but more details regarding indication
for testing, prior test results, and relevant family history can be found by examining
submitted documents. This information can help evaluate the appropriateness of the
incoming test order.
When a genetic abnormality has been identified in a family, it is common for fam-
ily members to seek testing for recurrence risk assessment for other children, for
subsequent pregnancies, or for relatives of the affected individual. In such instances,
all submitted records, reports, and notes on clinician communication prior to sam-
ple submission about the familial testing should be reviewed in detail to ensure that
the testing ordered is appropriate and consistent with clinician expectations. Due to
insurance or institutional contracts, it is also common for clinicians to seek testing
for family members through a different laboratory than that which originally tested
the proband. This introduces additional complexity and potential complications.
Differences in test methodologies between the two performing labs may be associ-
ated with discrepant mutation nomenclature, which could lead to the wrong region
being targeted during test setup. Also, differences in variant classification practices
between performing labs could lead to confusion with the interpretation and report-
ing of results for family members tested at different laboratories (Scacheri et al. 2008;
Kotzer et al. 2014). Therefore, it is important for the LBGC reviewing the arriving case
to pay close attention to the details of the family member’s result, ideally by review-
ing the family member’s original laboratory report. If the report is not available, the
LBGC may need to follow up with the clinician to discuss limitations of testing due
to potential variability in laboratory testing, interpretation, and reporting practices.
Box 8.1
Demographics—Assessment of patient sex and age can reveal potential misor-
ders. A blood sample for a 46-year-old male is received with an order for MECP2
gene analysis. Since the associated genetic condition, Rett syndrome, is X-linked
dominant and typically lethal in males, the patient age and gender alone can pro-
vide a clue to a potential misorder. The LBGC may suspect that the intended test
was for the RET gene (associated with multiple endocrine neoplasia syndrome
type 2) rather than Rett syndrome, which would be more plausible in the con-
text of an adult male patient. These type of misorders involving similar-sounding
genes, conditions, and/or tests occur commonly, and patient demographics can
serve as an initial indicator of these situations.
Sample Information—Sample type and gestational age for prenatal specimens can
affect testing assessment. For example, a laboratory receives a chorionic villus
sampling (CVS) specimen for Fragile X testing as the mother is a premutation
carrier. Due to concerns about the reliability of methylation testing on a CVS, the
LBGC contacts the clinician to review the benefits and limitations of perform-
ing Fragile X analysis on this sample type and to caution that, in the instance
of ambiguous results (i.e., repeat size borderline between premutation and full
mutation range), follow-up amniocentesis may be warranted. A potential expec-
tation gap was revealed by comparing the sample type and test requested.
Indication for Testing—When a clinician notes the indication for testing as
“rule out” a particular disorder, the potential for an expectation gap should be
explored. For example, a blood specimen on a pediatric patient is submitted for
chromosome microarray analysis with a testing indication of “rule out neurofi-
bromatosis.” As there are two types of neurofibromatosis, neurofibromatosis 1
(NF1) and neurofibromatosis 2 (NF2), which are clinically and genetically dis-
tinct, the LBGC contacts the clinician to discuss which type of neurofibromatosis
is of concern. NF1 can be caused by a deletion in a minority of cases, which would
be detectable by chromosome microarray, but most individuals with NF1 or NF2

have gene mutations not detectable by this assay. Unless there is clinical con-
cern for the typically more severe phenotype associated with the NF1 contiguous
gene deletion, if no prior testing has been done, the LBGC discusses the higher
diagnostic yield for gene sequencing as a first-tier test. In this example, the indi-
cation for testing, combined with the test requested, revealed an expectation gap
and potential test misorder.
Internal Laboratory Policy and Compliance Considerations

In addition to the thorough review of information provided on the requisition form
and included documents, the LBGC must be mindful of internal laboratory policies
or compliance considerations that may present barriers to the clinician’s testing plan
(Box 8.3). Such laboratory policies may include specimen criteria, requirements for
parental samples or parental test reports, or proband specimens for the purpose of a
Box 8.2
Review of Pending/Completed Results—A blood specimen for a pediatric patient is
submitted to assess for uniparental disomy (UPD) of chromosome 15. The clini-
cian has included normal results from methylation analysis for the Prader-Willi
and Angelman syndrome region. As a patient with UPD 15 would be expected
to have abnormal methylation studies, the UPD 15 testing appears to be a
test misorder. The LBGC calls the clinician to discuss the case and help iden-
tify other appropriate testing considerations depending on the clinical history.
The patient’s prior test results indicate that the testing chosen by the clinician
is unnecessary.
Review of Family Member Test Results—A blood sample is received for a pediatric
patient with developmental delay for chromosome microarray analysis. The sib-
ling is also affected and had microarray performed several years prior through
another institution, which identified a variant of uncertain significance. Upon
review of the sibling’s test report, it is evident that knowledge of this genomic
region has evolved and this copy number variation is now regarded as a benign
variant. The LBGC calls the clinician to explain that this variantwould no longer
be reported. Microarray remains indicated for this patient to investigate a poten-
tial cause for his delays as the siblings may have different etiologies, or in case an
updated, higher-density microarray platform could identify additional variants
not detectable by the previous microarray performed in the sibling. Thus, review
of family member test results revealed an expectation gap that could have led to
confusion in posttest counseling had the benign familial variant also been iden-
tified in the current patient but not reported.
Box 8.3
Internal Laboratory Policy—A cultured CVS specimen is submitted for testing for
an autosomal recessive disease. The mother is a known carrier but the father
has not been tested. The laboratory policy indicates that prenatal diagnosis for
an autosomal recessive condition is offered only when parental carrier testing
or diagnostic testing in an affected sibling has established the fetus to be at
25% risk. This ensures that targeted testing for known familial mutations can
be performed and prevents the possibility of ambiguous results (i.e., identifica-
tion of a variant of uncertain significance) that could occur if full gene analysis
were performed on a fetal specimen. The LBGC contacts the clinician to inform
him/her of the policy and to help identify potential solutions such as testing
the father or transferring the specimen to another laboratory that will perform
the assay without paternal carrier testing. Consideration of internal laboratory
policy compared with the testing ordered and prior family test results identified
a barrier to the clinician’s testing plan requiring immediate intervention.
positive control, along with billing and informed consent requirements (Scacheri et al.
2008). As discussed in Chapter 2, “Regulation of Laboratory Genetic Testing,” state-
specific issues can also be important to consider regarding laboratory licensure or
informed consent (Chen et al. 2009). Thus, the LBGC needs to be cognizant of where
the sample originated and if such laboratory license or consent requirements apply.
Additional policies on method of billing and required documents may also become
relevant.
Resolution of Pre-analytic Test Utilization Issues

As noted in the examples above, there are many circumstances in which the LBGC will
contact the clinician to resolve questions and concerns arising during pre-analytic test
utilization review or complications that evolve during the testing process. Chapter 12,
“Genetic Counselor Communication and Counseling Skills for the Laboratory,”
describes how genetic counseling communication skills are indispensable in such dis-
cussions. However, not only is effective communication imperative to successful reso-
lution, but the timeliness of contact with the clinician can be critical. Clinicians may
be difficult to reach quickly, and when there are concerns for inappropriate testing or
a critical expectation gap, the LBGC may need to decide whether to let the testing pro-
ceed as ordered or arrange for the specimen to be stabilized and place the testing on
hold until a discussion with the clinician can occur (Wain et al. 2012). Particularly in
the instance of prenatal or newborn testing, results may be needed rapidly for medi-
cal management. In such scenarios, the potential benefits and harms of holding the
test should be weighed carefully in the context of what is known about the patient’s
history and indication for testing (Balcom et al. 2016). When there is difficulty reach-
ing the clinician quickly, contacting an on-call physician or clinical support staff who
can find or reach the clinician urgently may be necessary. After discussion, the clini-
cian may decide to proceed with the testing as originally ordered. The LBGC should
be prepared to mitigate clinician frustration if the turnaround time has been affected
by a laboratory-induced hold. However, if discussion supports the need to change the
testing strategy, ultimately the timeline for accurate and informative results may be
improved.
Analytic Stage
CO M M U N I C AT I O N O F T E S T CO M P L I C AT I O N S A N D D E L AY S
Though the majority of samples will be processed without difficulty, unexpected com-
plications are possible with any assay and may require communication between the
LBGC and the clinician (Box 8.4). Repeat testing may be necessary if results do not
meet quality standards, whether this is related to technical difficulties or issues inher-
ent to the specimen. In some cases, even after multiple attempts, testing may fail,
meaning results do not meet quality control standards or are otherwise uninterpre-
table, and results cannot be issued (Scacheri et al. 2008). In the instance of test failure,
or when turnaround time is delayed, the clinician should be notified. The LBGC is well
positioned to communicate complex testing challenges to clinicians and to provide
Box 8.4
Communication of Test Complications and Delays—A saliva specimen is submitted
for BRCA1 and BRCA2 testing for a 42-year-old female patient with a personal
and family history of breast and ovarian cancer. If a pathogenic mutation is iden-
tified, a bilateral mastectomy and oophorectomy is planned versus a unilateral
mastectomy if results are negative. Unfortunately, the data do not meet quality
standards for reporting due to suspected DNA quality issues. As testing must be
repeated, test results may not be completed by the scheduled surgery date. The
LBGC contacts the clinicianto inform him/her of the anticipated delay for results
as this may affect surgery plans.
Fetal Sex Chromosome Result Discrepancy—A maternal blood sample is sent for
cell-free DNA aneuploidy screening at 20 weeks gestation due to the presence of
a soft marker for aneuploidy. The test requisition states that the fetus is female
by ultrasound; however, cell-free DNA sequencing results indicate the pres-
ence of Y chromosome material. In this instance, the LBGC contacts the clini-
cian to determine whether there was an error on the test requisition form or
possibly a misinterpretation of the external fetal genitalia on ultrasound. Once
it’s determined that there was not a clerical or ultrasound error, the LBGC can
help determine various biologic explanations for the presence of Y material in a
female fetus, such as the presence of an unbalanced translocation. The LBGC may
also discuss additional testing recommendations with the clinician, which could
include amniocentesis with microarray analysis.
updates on the status of testing. Timely and clear communication is essential as the
clinician depends on this information to adjust expectations with the patient.
Issues unrelated to data quality may also arise in the analytic stage requiring com-
munication with the clinician. Assays may evaluate patient sex as a quality control
metric or as part of genetic testing; however, the patient’s sex can be misreported on
test requisition forms. While a simple clerical error may easily explain an apparent
gender discrepancy, the possibility of a sample switch or sex chromosome abnormality
must be considered if not easily explained by a data entry error.
Post-analytic Stage
I N T E R P R E TAT I O N O F T E S T R E S U LT S
Often, clinical context is required to accurately interpret and report data generated
from genetic tests (Pfeifer 2006; Rehm et al. 2013). Review of clinical information is
integral to the interpretation process as it provides the indication for testing, aids in
determination of which results are clinically significant, guides follow-up testing rec-
ommendations, and allows for accurate risk assessment in the case of negative results
(Scacheri et al. 2008; Wain et al. 2012). Clinical information also helps laboratory staff
Box 8.5
Result Interpretation in the Context of Indication for Testing—ATP7B full gene
sequencing is ordered to assess for Wilson disease, an autosomal recessive con-
dition. A single heterozygous mutation is identified. The interpretation of this
result depends on the indication for testing. If the indication for testing is to
assess carrier status, this is a conclusive result consistent with positive carrier
status for Wilson disease. If, however, the indication for testing is to rule out a
diagnosis of Wilson disease, this result is not definitive. The presence of a hetero-
zygous ATP7B mutation may increase the likelihood of a diagnosis of Wilson dis-
ease, but it neither proves nor excludes the diagnosis. Therefore, the interpretive
section of the final report for this patient depends on the indication for testing.
identify situations in which test results are discordant with the patient’s clinical pre-
sentation, potentially indicating a sample mix-up or laboratory error.
Correlation of Indication for Testing with Test Result

The indication for testing has a significant impact on the interpretation of genetic
testing results (Box 8.5). Knowing whether testing is being ordered for carrier
screening versus diagnostic testing purposes, whether or not the patient is symp-
tomatic, and whether or not the patient has a family history of the genetic condition
being tested will all affect the test interpretation. LBGCs are well equipped to assist
with the correlation of genetic test results and clinical information for proper inter-
pretation of the data. At this stage of the testing process, the LBGC may need to
contact the clinician to obtain additional clinical information based on the observed
results.
Determining Clinical Significance of Results

Accurate and comprehensive patient clinical information is especially important to

the interpretation of genomic, nontargeted testing. Chromosomal microarray and
whole exome/genome sequencing generate vast amounts of data that must be fil-
tered down to the most relevant, reportable results. One part of that process involves
using algorithms to determine the potential pathogenicity of various findings (for
more detail see Chapter 4, “Cytogenetic Technologies and Test Issues,” and Chapter 5,
“Molecular Technologies and Test Issues”), but that information must be interpreted
in the context of the patient’s clinical features and the indication for testing, which
can allow the laboratory to distinguish between primary and unintended, secondary
results. Clinical information may affect the determination of the clinical significance
of genomic test results and may make the difference in deciding whether a particular
finding is included in the report (Box 8.6).
Accurate Risk Revision

For certain tests, clinical information may allow the laboratory to provide accurate
risk revision as part of the test interpretation process (Box 8.7). Patient ethnicity,
Box 8.6
Determining Clinical Significance of Results—A sample is received for whole exome
sequencing. Review of the requisition form by the LBGC shows that the patient’s
clinical phenotype includes dilated cardiomyopathy, among other clinical fea-
tures. When reviewing testing results, a novel missense change in the DNAJC19
gene is noted. Although the pathogenicity of this variant cannot be definitively
determined based on the lack of reported data, this gene is reported to be asso-
ciated with dilated cardiomyopathy. Based on this association, the laboratory
decides to report this finding as a variant of uncertain clinical significance in a
gene related to the patient’s reported clinical phenotype.
family history, and reproductive partner carrier status may all influence the laborato-
ry’s risk assessment. With their background training in quantitative risk assessment,
LBGCs are able to integrate this clinical information into the risk revision provided in
the final report.
Identification of Potential Testing Errors

Having sufficient clinical information also helps the laboratory identify testing
errors by recognizing situations where test results may not fit the clinical picture
or where results appear to be discrepant. LBGCs can play a key role in identifying
potential errors due to their knowledge of the clinical context of the cases in the
laboratory and can also assist in obtaining necessary clinical information to pro-
vide a potential explanation for apparently discrepant lab results. The examples
in Box 8.8 illustrate the utility of clinical information for identifying or resolving
potential testing errors.
Box 8.7
Accurate Risk Revision—For CF targeted testing, the residual risk associated
with a negative result depends on the patient’s ethnicity and family history.
For example, a targeted mutation panel is associated with a detection rate of
91% for patients of Northern European ancestry (Farrell et al. 2008). If a sam-
ple from a patient of this ethnicity is submitted for carrier screening and no
family history is noted on the paperwork, the residual risk to be a carrier asso-
ciated with a negative result would be assigned as approximately 1/260 (based
on a carrier frequency of 1/25 in this population). If, however, the paperwork
accompanying the sample indicates that the patient’s first cousin is affected
with CF (mutations unknown), the residual risk associated with a negative
result would be modified to 1/35 using Bayesian analysis, since the a priori risk
for the patient to be a carrier has increased to 1/4 based on the family history
information.
Box 8.8
Clinical Information Does Not Match Results—A sample is sent for MSH2 tar-
geted testing for a familial mutation and results are negative. Without clinical
information, this result would be reported as a “true negative” result indicat-
ing that the patient does not have an elevated risk for Lynch syndrome–related
cancers. However, if the laboratory was provided with additional information
indicating that the patient being tested was diagnosed with colon cancer at age
30, the LBGC would likely be suspicious of a negative result in this context. The
LBGC may then initiate additional investigation into the case to confirm that the
correct familial mutation was provided, that the correct region of the gene was
analyzed to capture that mutation, and that a sample mix-up has not occurred,
either within the laboratory or at the site of the blood draw.
Result Discrepancy—A sample is sent for alpha-1-antitrypsin (A1AT) deficiency
testing in which both quantitative A1AT serum analysis and genotyping are per-
formed. A ZZ genotype is identified, consistent with A1AT deficiency. Typically
this genotype would be associated with reduced A1AT activity. In this case, how-
ever, the patient’s A1AT serum level is 120 mg/dL, much higher than would be
expected in the context of a ZZ genotype. Before the laboratory initiates additional
testing to resolve the apparent discrepancy, the LBGC may be able to obtain addi-
tional clinical information that would account for the lab results, such as a prior
transplant history or current treatment with augmentation therapy (infusion with
purified A1AT to elevate deficient serum A1AT), both of which would be expected
to be associated with a discrepancy between genotype and A1AT serum levels.
Follow-Up Testing Recommendations

Understanding the patient’s clinical history also allows the laboratory to make more
specific follow-up testing recommendations as part of test interpretation. This may be .
conveyed through the final test report or through a phone call from the LBGC to the
clinician to discuss follow-up testing recommendations (Box 8.9).
Box 8.9
Recommendation for Follow- Up Testing— A methylation- sensitive multiplex
ligation-dependent probe amplification (MS-MLPA) assay targeting the 11p15
imprinting center regions is an appropriate test for patients being considered
for a diagnosis of Beckwith-Wiedemann syndrome (BWS) or Russell-Silver syn-
drome (RSS). In the case of negative results, if the indication for testing is to
rule out BWS, follow-up with CDKN1C gene sequencing would be appropriate.
If, on the other hand, the indication for testing is to rule out RSS, it would be
appropriate instead to recommend follow-up uniparental disomy (UPD) analysis
for chromosome 7.
R E P O R T I N G O F T E S T R E S U LT S
Drafting of Report Verbiage
Once results of testing are complete, LBGCs are often involved in using the available
clinical information to determine appropriate verbiage for the final report (Christian
et al. 2012; Waltman et al. 2016). Common indications for testing can be anticipated
by the laboratory, and LBGCs may help develop standard interpretation comments
for each anticipated indication for testing and result, thus increasing the efficiency of
the reporting process and promoting consistency. To apply a standard reporting com-
ment, sufficient clinical information must be obtained for incoming samples, which is
typically reviewed by LBGCs as discussed earlier in this chapter. Not all cases will fit
the standard reporting scenarios, and these exceptions will require more individual-
ized comments, which can also be drafted or reviewed by LBGCs. For example, an
LBGC may be involved in developing a reporting framework for a single gene sequenc-
ing assay. Some report fields, such as the method and any relevant test disclaimers,
will likely be standard across all reports. Others, such as the result and interpreta-
tion, can be formatted in a consistent fashion across reports and may have standard
verbiage in some cases (e.g., for negative results), but for a positive result the report
would likely require some amount of manual entry. In the case of a particularly com-
plex result, such as a variant of uncertain significance but with a large amount of pub-
lished data regarding its potential pathogenicity or benign status, an LBGC involved
in report writing may spend a significant amount of time crafting an interpretation
that conveys all of the necessary details pertaining to the identified variant in a clear
and organized fashion.
Calling Out Results

Upon completion of testing, an LBGC may be involved in informing the clinician of
the results and addressing any questions. This conversation can include recommenda-
tions for additional testing. Such communication may be initiated by either the LBGC
or the clinician.
LBGCs may use information about the patient to determine which cases warrant
calling the clinician or laboratory with results. This could include results that are par-
ticularly time-sensitive, such as prenatal test results or results that are being used to
dictate medical intervention for the patient. Unexpected test results may also war-
rant a phone call to the clinician, such as a hexosaminidase enzyme test ordered for
carrier screening purposes that reveals enzyme levels in the affected range. LBGCs
may also call out results if there is a high risk of misinterpretation, such as a variant
of uncertain significance that could have negative implications for the patient if its
significance is overestimated or underestimated by the clinician.
In addition to using patient-specific clinical information to guide decisions about
which results to call out, LBGCs may infer this from pretest communication with the
clinician. These conversations may offer insight into the clinician’s familiarity and
comfort level with interpreting genetic test results. If the clinician has indicated rela-
tive unfamiliarity with genetic testing, the LBGC may determine that calling to discuss
results would be helpful to ensure comprehension and offer guidance for follow-up.
L O N G -T E R M F O L L O W -U P
LBGCs may also be involved in follow-up activities beyond the initial results dis-
closure. Given the pace with which the field of genetics is advancing, situations can
occur that present an opportunity for long-term follow-up, including reclassification
of variants of uncertain clinical significance; reanalysis of whole exome/genome or
microarray data; or repeat testing of previously negative patients due to updated test
methodologies. Who, if anyone, should be responsible for initiating this long-term
follow-up has been the subject of much debate and has been labeled as the “duty to
recontact.” This is a complex situation involving many parties, including primary care
providers, specialists such as medical geneticists, laboratory staff, and patients. While
the American College of Medical Genetics and Genomics’ “duty to recontact” policy
statement puts the onus on the primary care provider and the patient, a 2014 sys-
tematic literature review revealed a sentiment that laboratory staff have a “particular
duty” to inform healthcare providers of changes in test interpretations (Hirschhorn
et al. 1999; Otten et al. 2015). And guidelines from the American College of Medical
Genetics and Genomics, as well as the College of American Pathologists’ accrediting
regulations, specify that laboratories document their own policies regarding reevalua-
tion, reanalysis, and recontact (Richards et al. 2015; College of American Pathologists
n.d.). LBGCs can play a key role in facilitating these processes and providing clear
and timely communication to clinicians, whether initiated by the laboratory or the
clinician.
Some types of laboratories, including biochemical, newborn screening, and cell-
free DNA laboratories, may be interested in additional clinical outcome information
to ascertain correlations between certain results and clinical phenotype in order to
refine assay reference ranges. For example, in the case of fetal cell-free DNA aneu-
ploidy screening, some laboratories have an “intermediate/borderline positive” result
category. The LBGC may be involved with contacting the clinician after delivery to
obtain birth outcome information for cases of borderline results in an attempt to bet-
ter determine the likelihood of these results to be true positives or false positives. All
long-term follow-up scenarios can be complicated by the fact that patients may have
changed clinicians during the time between testing and follow-up. And even if the
patient is still being seen at the facility where testing was ordered, busy clinicians may
have less capacity to provide follow-up information that does not directly pertain to
testing that is in progress. In these situations, LBGC communication skills are essen-
tial to obtain the necessary information.
Future Directions
Complex testing strategies, nuances of results interpretation, and a general lack of
genetics knowledge among healthcare providers create significant barriers to the
appropriate use of genetic testing. This is likely to become more pronounced with the
development of newer testing methodologies, which will require even more detailed
pretest and posttest counseling and the potential for even greater gaps in healthcare
providers’ expectations. LBGCs will need to identify and mitigate these expectation
gaps by routinely communicating with clinicians.
Another way in which LBGCs can address the complexities of genetic testing is
to provide direct communication with patients. A few laboratories are beginning to
offer direct patient counseling services provided by LBGCs to facilitate both upfront
risk assessment and informed consent for genetic testing, as well as posttest results
disclosure and counseling (Waltman et al. 2016). This is a model that may expand
with the increasing complexities of genetic testing and the need for proper pretest and
posttest counseling.
Before LBGCs communicate results to clinicians and/or patients, the data must
be accurately and efficiently interpreted. As whole genome tests are used more regu-
larly, LBGCs are likely to become more involved with interpretation of genomic data.
LBGCs can perform roles in the whole genome arena such as the clinical correlation
of variants given their combined knowledge of genetics and their clinical expertise
(Swanson et al. 2014). In addition to the increasing utility of whole genome tests
for the identification of germline mutations to diagnose disease and assess recur-
rence risks, genetic tests for the molecular characterization of tumors and selection
of targeted therapies are also expanding. The majority of examples used throughout
this chapter pertain to LBGCs’ involvement in case management of genetic testing
for germline mutations. However, LBGCs’ skills are increasingly being applied in the
areas of somatic mutation analysis and pharmacogenomics tests, as there are similar
case management needs.
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Practical Genetic Counseling For The Laboratory - (8. Genetic Counselor Role in Laboratory Case Management)

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Practical Genetic Counseling For The Laboratory - (8. Genetic Counselor Role in Laboratory Case Management)

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8

Genetic Counselor Role in Laboratory Case

As liaisons between laboratory personnel and external clients, genetic counselors in

Pre-analytic Analytic Post-analytic

Prior to Sample Receipt

Upon Sample Receipt

Figure 8.1 LBGC involvement across the stages of genetic testing.

of sendout testing if multiple assays must be performed on such limited specimens.

Review of the Requisition Form

Review of Prior Test Results, Family History, and Clinical Notes

be detectable by chromosome microarray, but most individuals with NF1 or NF2

Internal Laboratory Policy and Compliance Considerations

Resolution of Pre-analytic Test Utilization Issues

Correlation of Indication for Testing with Test Result

Determining Clinical Significance of Results

Accurate and comprehensive patient clinical information is especially important to

Accurate Risk Revision

Identification of Potential Testing Errors

Follow-Up Testing Recommendations

Calling Out Results

You might also like

Practical Genetic Counseling For The Laboratory - (8. Genetic Counselor Role in Laboratory Case Management)

Uploaded by

Document Information

Original Title

Copyright

Available Formats

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Sharing Options

Did you find this document useful?

Is this content inappropriate?

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Available Formats

Practical Genetic Counseling For The Laboratory - (8. Genetic Counselor Role in Laboratory Case Management)

Uploaded by

Copyright:

Available Formats

8

Genetic Counselor Role in Laboratory Case

As liaisons between laboratory personnel and external clients, genetic counselors in

Pre-analytic Analytic Post-analytic

Prior to Sample Receipt

Upon Sample Receipt

Figure 8.1 LBGC involvement across the stages of genetic testing.

of sendout testing if multiple assays must be performed on such limited specimens.

Review of the Requisition Form

Review of Prior Test Results, Family History, and Clinical Notes

be detectable by chromosome microarray, but most individuals with NF1 or NF2

Internal Laboratory Policy and Compliance Considerations

Resolution of Pre-​analytic Test Utilization Issues

Correlation of Indication for Testing with Test Result

Determining Clinical Significance of Results

Accurate and comprehensive patient clinical information is especially important to

Accurate Risk Revision

Identification of Potential Testing Errors

Follow-​Up Testing Recommendations

Calling Out Results

You might also like

Resolution of Pre-analytic Test Utilization Issues

Follow-Up Testing Recommendations