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Laposata's Laboratory Medicine Diagnosis of Disease in Clinical Laboratory - 3rd Edition Full Download

The document discusses key concepts in laboratory medicine, including the definitions and implications of positive and negative predictive values, the differences between prevalence and incidence, and the importance of precision versus accuracy in test results. It highlights the phases of laboratory analysis, common errors, and the significance of patient preparation and specimen handling in obtaining accurate test results. Additionally, it emphasizes the need for careful test selection and interpretation to minimize medical errors and improve patient outcomes.
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0% found this document useful (0 votes)
220 views17 pages

Laposata's Laboratory Medicine Diagnosis of Disease in Clinical Laboratory - 3rd Edition Full Download

The document discusses key concepts in laboratory medicine, including the definitions and implications of positive and negative predictive values, the differences between prevalence and incidence, and the importance of precision versus accuracy in test results. It highlights the phases of laboratory analysis, common errors, and the significance of patient preparation and specimen handling in obtaining accurate test results. Additionally, it emphasizes the need for careful test selection and interpretation to minimize medical errors and improve patient outcomes.
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Laposata's Laboratory Medicine Diagnosis of Disease in

Clinical Laboratory 3rd Edition

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The Definition of Predictive Value of a Positive Test

The population of individuals with a positive test result is the focus of positive predictive value. The positive predictive value for a laboratory test
indicates the likelihood that a positive test result identifies someone with disease. It should be noted that the predictive value of a positive test is
greatly influenced by the prevalence of the disease in the area where testing is performed. As an example, a screening test for HIV infection is more
likely to be confirmed as positive in an area where many individuals are infected with HIV, as opposed to a location where there is only a rare case of HIV
infection. In the latter situation, most of the positive HIV tests in the initial evaluation of a patient are found to be false­positives by confirmatory tests. A
high percentage of false­positives from a low prevalence disease, as shown in the following formula, decreases the predictive value of the positive test:

true­positivestrue­positives+false­negatives×100
The positive predictive value for a laboratory test indicates the likelihood that a positive test result identifies someone with
disease. The negative predictive value for a laboratory test indicates the likelihood that a negative test result identifies someone
without disease.

True­positives and false­positives are the groups with a positive test result; as noted above, positive predictive value focuses on those with a positive
test.

The Definition of Predictive Value of a Negative Test

The population of individuals with a negative test result is the focus of the negative predictive value. The negative predictive value for a laboratory test
indicates the likelihood that a negative test result identifies someone without disease. It is not greatly influenced by the prevalence of disease because
false­positives are not included in the formula for negative predictive value. The formula for predictive value of a negative test result is:

true­negativestrue­negatives+false­negatives×100
True­negatives and false­negatives are the groups with a negative test result; as noted above, negative predictive value focuses on those with a
negative test result.

The Difference Between Prevalence and Incidence

The prevalence of a disease reflects the number of existing cases in a population. It is usually expressed as a percentage of a certain population.
Incidence refers to the number of new cases occurring within a period of time, usually 1 year. For example, in the United States, sore throat has a low
prevalence because considering the size of the population there is a low percentage of individuals at a given time afflicted with sore throat. However, it
has a high incidence because many new cases of sore throat appear each year.

Precision versus Accuracy

Precision refers to the ability to test one sample and repeatedly obtain results that are close to each other. This does not infer that the mean of these
very similar numbers is the correct number (see Figure 1–5). Some analyses, which have great precision, are very inaccurate. The accuracy reflects the
relationship between the number obtained and the true result. Thus, a sample could have high accuracy but low precision if it provides the correct
answer but has substantial variability as the sample is repeatedly tested.

FIGURE 1–5

A series of “bulls­eye” illustrations that display excellent or poor precision and accuracy.
Precision refers to the ability to test one sample and repeatedly obtain results that are close to each other. This does not infer that
the mean of these very similar numbers is the correct number.

Analyzing Errors in Laboratory Performance

There are three phases of laboratory analysis. The first of these is the preanalytical phase. This time frame is from patient preparation for the
laboratory test, through the time of sample collection, until the sample arrives in the laboratory. Most of the errors in laboratory test performance
occur in this phase. Examples of preanalytical errors are inappropriate preparation of the patient, such as not fasting for a particular test in which
fasting is required; ingesting drugs that will interfere with the laboratory tests; collection of the specimen in the wrong tube; delayed transport of the
specimen to the laboratory; storage of the sample at an incorrect temperature; and collection of an inadequate amount of blood in vacuum tubes
containing a fixed amount of anticoagulants. All these errors occur before the sample arrives for analysis and make it impossible, no matter how great
the analytical precision within the laboratory, to provide a test result that truly reflects the patient's condition. The second phase is the analytical
phase, which is the time that the sample is being analyzed in the laboratory. Errors can occur during this process, but they are much less common now
because of the high level of automation of many laboratory instruments. Examples of analytical errors are incorrect use of the instrumentation and the
use of expired reagents. The third phase of laboratory test performance is the postanalytical phase, which begins when the result is generated and
ends when the result is reported to the physician. Examples of errors in this phase, which are more common than analytical errors but less common
than preanalytical errors, are delay in time to enter a completed result into the laboratory information system and reporting results for the wrong
patient.

Minimizing Errors in the Selection of Laboratory Tests

As the number of laboratory tests has increased in size, complexity, and cost, health care providers are highly challenged to select the correct tests, and
only the correct tests, in pursuit of a diagnosis. One approach commonly implemented to assist physicians in correct test selection is the use of a reflex
test algorithm. Tests are ordered by algorithm selection, such as selection of an algorithm to determine the cause of a prolonged PTT result. Using the
algorithm, the clinical laboratory notes the results of the first test in the algorithm, and that result determines which test is performed next. For
example, if the prolonged PTT is further evaluated with a PTT mixing study, a normal result would direct testing toward assays for factors VIII, IX, XI, and
XII. An elevated result in the PTT mixing study, on the other hand, would direct testing toward an inhibitor in the PTT reaction, such as a lupus
anticoagulant. Testing is continued within the algorithm until a diagnosis, which explains the prolonged PTT in this case, is identified.

b l i i l d diffi l b l b h d d h l df
Laboratory test selection is also made more difficult because many laboratory tests have synonyms, and many compounds have related forms. For
example, the test most commonly known as the lupus anticoagulant is also called the lupus inhibitor, and the general term that includes the lupus
anticoagulant and related entities is antiphospholipid antibody. Vitamin D has several isoforms that include 25­hydroxyvitamin D and 1,25­
dihydroxyvitamin D. Incorrect laboratory test selection is a major source of medical error.

Minimizing Errors in the Interpretation of Laboratory Test Results

With thousands of tests on the clinical laboratory test menu, it is impossible for a health care provider to understand the clinical significance of an
abnormality for each test. This has become particularly noteworthy with the introduction of tests for genetic alterations, because there are so many
and the clinical significance of the alterations may not yet be well established. In some institutions, narrative interpretations of complex clinical
laboratory evaluations are prepared by experts in the field. In most institutions, such narratives require a special request for completion, but an
emerging concept is to provide narrative interpretations for all complex clinical laboratory evaluations automatically, as they are provided in radiology
and in anatomic pathology. Misinterpretation of laboratory test results has been increasingly noted as a source of poor patient outcome.

PREANALYTICAL VARIABLES THAT AFFECT LABORATORY TEST RESULTS


The Effect of Age on Laboratory Tests

There are a number of laboratory tests that have different normal ranges for patients of different ages. This is particularly important in pediatrics.
Newborns especially have many different normal ranges than adults or older children for substances in blood and other bodily fluids. For example,
several of the coagulation factors do not reach adult levels for many months after birth. As a second well­known example, the cholesterol level rises
with age.

The Effect of Gender on Laboratory Tests

Gender has a significant bearing on many laboratory tests. Testosterone and estradiol are obvious examples. In addition, among women there are
variations in the serum concentration of various hormones throughout the menstrual cycle.

The Effect of Body Mass on Laboratory Tests

Muscle mass can affect the level of certain compounds, such as creatine kinase, in the blood. It is also known that there is an increase in the serum
cholesterol level with obesity, because the cholesterol level is related to the amount of body fat.

Preparation of the Patient for Laboratory Testing

For certain laboratory tests, there are a number of special preparations of the patient that are necessary to provide the most clinically useful, accurate,
and precise result. One of the most commonly encountered patient preparations is fasting, usually for 8 to 12 hours, depending on the test. The serum
triglyceride level can be significantly affected by eating, and fasting is absolutely required. Another test for which fasting is required is the fasting blood
glucose used in the evaluation of a patient for diabetes.

One of the most commonly encountered patient preparations is fasting, usually for 8 to 12 hours, depending on the test. The serum
triglyceride level can be significantly affected by eating, and fasting is absolutely required. Another test for which fasting is
required is the fasting blood glucose.

Patient Posture for Blood Collection

Patient posture may affect the result for certain tests. There is a lower plasma volume when the patient is upright because there is pooling of fluid in
the dependent parts of the body when standing. When the patient is supine, there is a movement of fluid back into the circulation from the tissues. The
extra volume in the circulation can dilute certain compounds in the blood. It is best to monitor the patient in the same postural position if the test
result is affected by posture and if the values need to be compared with one another over time.

Differences in Test Results Between Samples of Venous, Arterial, and Capillary Blood
p , , p y

Venous blood may have a different concentration of a compound than arterial blood. The best examples are the blood gases that show marked
differences between arterial and venous blood because of the exchange of gases in the lungs. There may also be a difference between capillary blood
and arterial and venous blood. Blood glucose values may differ significantly in capillary (finger­stick) samples from venous or arterial blood.

INTERFERENCES IN LABORATORY TESTS


Analytical Interferences in Laboratory Testing

Interferences may result in falsely high or falsely low values, depending on the interfering substance and the particular test. Although there are many
compounds that can interfere with the accurate and precise quantitation of a compound, there are three major interferences that must be considered
when selecting and interpreting results of laboratory tests. These are hemolysis that makes plasma and serum red; elevated bilirubin that makes
plasma and serum shades of orange, green, or brown; and lipemia that makes plasma and serum milky white. There are many drugs, particularly those
that color the plasma and serum, that can produce significant analytical interference. Many automated laboratory tests are spectrophotometric, and
therefore depend on measurable changes in the color of plasma or serum after a chemical reaction. This is why alterations in the color of the serum or
plasma often interfere with laboratory test performance.

There are three major interferences that must be considered when selecting and interpreting results of laboratory tests. These are
hemolysis that makes plasma and serum red; elevated bilirubin that makes plasma and serum shades of orange, green, or brown;
and lipemia that makes plasma and serum milky white.

Impact of Drugs on Laboratory Test Results

Drugs can affect laboratory tests in two ways—as an interfering substance in the laboratory test only and by producing an effect in the body that alters
a laboratory test result. For example, there are many drugs that will increase the PT in patients receiving warfarin (coumadin) by an in vivo potentiation
or diminution of warfarin­induced anticoagulation. There are a number of drug effects, however, that alter the result of a particular test strictly in vitro,
and do not change anything in vivo.

TEST SELECTION GUIDELINES


The Use of Screening Tests Before Esoteric Tests

Screening laboratory tests are typically inexpensive, easy­to­perform assays that indicate whether additional tests need to be performed to reach a
diagnosis. Whenever possible, if a screening test is available, it should be used before the more expensive or time­consuming tests are performed. An
example of the use of a screening test is the partial thromboplastin time (result within minutes/hours and at low cost) to assess a major portion of the
coagulation cascade. Only if this value is elevated should tests be performed for PTT­related coagulation factor deficiencies (results within several
hours and at high cost).

The Danger of Ordering Too Many Laboratory Tests

As noted in the discussion of the normal range, 5% of individuals who have no disease can fall outside of the reference range established by the central
95% of healthy individuals. Thus, if an individual without disease has 20 different tests, it is likely on a statistical basis that he/she will have 1 abnormal
value (5% = 1 of 20). In medical practice, the abnormal test result for the normal patient often leads to further evaluation and raises suspicion for a
disease that does not exist. Thus, by limiting the number of tests ordered for a patient to those relevant to the clinical presentation of the patient, one
is less likely to encounter false­positive or false­negative results.

SPECIMEN PROCESSING AND HANDLING


The Importance of Turnaround Time

An accurate and precise laboratory test result provided after a decision has been made regarding patient management is of no value. Since results for
all laboratory tests cannot be provided immediately, the physicians and laboratory personnel must decide on clinically relevant turnaround times for
hl b ddi i if i i di h df h h i lb f d l i l b i hi h i ifi
all laboratory tests cannot be provided immediately, the physicians and laboratory personnel must decide on clinically relevant turnaround times for
each laboratory test. In addition, if a patient is not discharged from the hospital because of a delay in laboratory testing, this may have a significant
financial impact from unnecessary length of stay. All steps related to turnaround time, from ordering of the test to the reporting of the result, must be
carefully analyzed and shortened as much as possible.

Tubes for Blood Collection

There are a number of different tubes into which blood may be collected. The tubes used for the vast majority of collections contain a vacuum to help
draw the blood into the tube. The tops of the tubes have a different color depending on the contents of the tube prior to blood collection (Table 1–1).
Several of the tubes contain anticoagulants to prevent the clotting of the blood in the tube. Clotted blood that is centrifuged to remove the clot and any
cells is known as serum. Blood that has not been clotted and is then centrifuged to remove any cells is known as plasma. For many laboratory tests, the
same result is obtained in an assay if serum or plasma is used. However, this is often not the case. The clotting of the blood, for example, makes blood
cell counts and coagulation tests impossible because the clotting factors are consumed in the clot and the blood cells become trapped in it. If the
clotting of the blood to form serum is not absolutely necessary, tests can be performed with a shorter turnaround time using plasma because there is
no requisite time to wait for the blood clot to form. The amount of anticoagulant in the light blue­top tube must be in a specific proportion to the blood
volume in the tube, usually 9 parts blood to 1 part citrate solution. When an inadequate amount of blood is collected into a blue­top tube, the ratio of
blood to anticoagulant is less than 9:1. This can result in spuriously high values for the PT and PTT tests. Thus, light blue­top tubes must be filled
appropriately to obtain accurate results for clotting tests.

TABLE 1–1
Cap Color and Contents of Tubes for Blood Collection

Cap Color Contents

Red Nothing—the sample clots and the product is serum

Light blue Citrate anticoagulant

Purple (lavender) EDTA anticoagulant

Green Heparin anticoagulant

Red/Green with gel No anticoagulant, but a gel is present that separates the serum or plasma and the cells after centrifugation

Gray Fluoride (glycolysis inhibitor for optimum glucose measurements) with oxalate anticoagulant

Yellow Acid­citrate­dextrose solution (ACD) that anticoagulates the blood and helps preserve the blood cells during processing

Dark blue Nothing—but the tube is specially treated to permit accurate measurement of trace heavy materials

Clotted blood that is centrifuged to remove the clot and any cells is known as serum. Blood that has not been clotted and is then
centrifuged to remove any cells is known as plasma.

Timing of Blood Collection

Patients may have a need to present for phlebotomy at a certain time of the day if the parameter being measured has a diurnal variation in its
concentration.

Dynamic tests involve the measurement of a patient response to a treatment or stimulus, and timing of collection is important in these studies. The
oral glucose tolerance test, in which plasma glucose levels are measured after the oral ingestion of a glucose solution, is an example of such a test.

A third situation in which timing of sample collection is important is in therapeutic drug monitoring. The serum level of certain drugs is measured to
A third situation in which timing of sample collection is important is in therapeutic drug monitoring. The serum level of certain drugs is measured to
determine if the concentration is within the therapeutic window. The serum level of a drug varies greatly as the drug is absorbed, distributed, and
metabolized, so the timing of collection must be consistent. For the monitoring of many drugs, a “trough” level is obtained just before the next dose of
the drug is administered.

EFFECTS OF CELL INJURY AND INFLAMMATION ON SELECTED LABORATORY TESTS


The Release of Plasma Markers of Organ Damage from Injured Cells

When cells are injured, components of the cells can leak out of the damaged or dead cells and make their way into the systemic circulation. This
permits the measurement of these “marker” compounds in the serum or plasma as a test for injury to the organ. The most important features of
plasma markers of cell injury are that (1) they are not rapidly removed from the circulation; (2) they are relatively organ specific so that the damaged
organ is identified; and (3) the compound is precisely and accurately measured in the clinical laboratory. A well­known example includes the release of
the creatine kinase­MB fraction and troponin from myocardial cells injured by ischemia in myocardial infarction.

Markers of Inflammation and the Acute­Phase Response

The concentration of many plasma proteins changes significantly in patients with inflammation. Infections (even minor viral illnesses), autoimmune
disorders, and many other conditions result in an increased concentration of proteins known as acute­phase reactants. Commonly used tests to
assess the severity of inflammation, from whatever cause, are the erythrocyte sedimentation rate (ESR) and C­reactive protein (CRP). Examples of
acute­phase reactant proteins include fibrinogen, which can rise as much as 10­fold over baseline, and von Willebrand factor, which can rise 2­ to 3­
fold over baseline. The rise in von Willebrand factor with inflammation can mask a deficiency of von Willebrand factor in patients with von Willebrand
disease, and this highlights the need to obtain baseline values after an acute­phase response subsides for accurate diagnosis.

When cells are injured, components of the cells can leak out of the damaged or dead cells and make their way into the systemic
circulation. This permits the measurement of these “marker” compounds in the serum or plasma as a test for injury to the organ.

The Serologic Diagnosis of Infectious Disease

It is not uncommon to suffer an infection with an organism that is not identifiable by Gram staining or other microscopic analysis and is not readily
cultured. For these infections, the diagnosis is often made by identifying and measuring the amount of antibody produced in response to an antigen
derived from the infectious agent. The antibody response typically takes several days to a week or two (dependent on past exposure) to emerge, and
the appearance of IgM antibody before IgG occurs in most infections. This is why the presence of IgM antibody in a serologic test is likely to reflect an
acute infection rather than past exposure. Serologic tests may also be designed to detect and measure an antigen associated with the infectious agent.
This obviates the inherent delay in diagnosis of the infection of up to approximately 2 weeks while waiting for the antibody response to occur.

MOLECULAR TESTING
Overview

There is an increasing amount of genetic information used to establish a diagnosis, and there is limited understanding by the majority of practitioners
about the genetic terminology which appears in the patient record. This section will attempt to clarify the terminology associated with the
identification of genetic variations in tumors and in non­tumor tissue at both the gene level and at the level of the protein. This section will also present
information about the genetic variations associated with poor responses to therapeutic drugs, also called pharmacogenomics. Finally, there will be a
section to describe the molecular results from tests used to identify infectious organisms.

Genetic Structure and Function

Humans have more than 20,000 genes, and each human has many alterations when compared to a sequence established as normal. There are multiple
reference sequences in use. The most frequently used reference is a “coding DNA reference sequence,” and that is the reason why the changes at the
DNA level are sometimes described starting with “c.” The genetic sequence building blocks are four nucleotides—adenine (A), guanine (G), cytosine (C),
and thymine (T). Individual genes contain segments called exons which code for a protein. The segments between the exons, which do not code for a
DNA level are sometimes described starting with c. The genetic sequence building blocks are four nucleotides—adenine (A), guanine (G), cytosine (C),
and thymine (T). Individual genes contain segments called exons which code for a protein. The segments between the exons, which do not code for a
protein, are called introns.

Genetic variations can result in the exchange of one nucleotide for another, the deletion of one or more nucleotides, the insertion of one or more
nucleotides, or other complex changes. Most changes in an exon of a gene will result in a change in the amino acid sequence of the protein associated
with that gene. Therefore, changes in the gene can result in the exchange of one amino acid for another, the deletion of one or more amino acids, the
insertion of one or more amino acids, or if the change in the genetic code introduces a stop codon, protein synthesis will be truncated before synthesis
is complete.

The commonly used term “mutation” is synonymous with “genetic variation” which is being increasingly used because patients are concerned about
being designated as a “mutant.” There is also confusion about the difference between mutation and polymorphism. A mutation is associated with
disease, and is present in less than 1% of individuals. A polymorphism represents a genetic variation because it is different from the “normal”
comparator genetic code, but it is not associated with a disease. A polymorphism is found in more than 1% of individuals. Mutations can arise
spontaneously in any cell. When they appear in cells other than germ cells (eggs and sperm), they are called somatic mutations. For example, many
mutations in tumors are somatic mutations because they are not present at birth. The opposite term is a germline mutation. As noted by the name,
these mutations are in the patient's germ cells, and these mutations can be inherited. Importantly, even though mutations can be associated with
disease, the effect of a mutation may remain silent or contribute to the development of active disease.

Genetic Variations/Mutations

When patients do not have a mutation for which they have been tested, the results in a patient report read “no mutation detected,” “wild type,” or
“normal.” The following example provides a description of an alteration in which there has been a substitution of one nucleotide for another. This
results in a change of one amino acid. In this example, the colloquial name of the mutation is the factor V Leiden mutation, and there are numerous
colloquial synonyms. One synonym is “activated protein C resistance mutation, Leiden type.” The genetic variation that produces this mutation is a
replacement of a guanine for an adenine at position 1691 within the gene. It is written as 1691G>A, and represents a single nucleotide variant (SNV), a
term which is preferred over single nucleotide polymorphism (SNP). It is also written as c.1691G>A because the use of the “c” indicates that the change
is at the DNA level. The change at this position in the gene results in a change in the amino acid at position 506 for the factor V protein. An arginine
residue is substituted for by a glutamine residue. This is written as Arg506Gln using the three­letter code for an amino acid, or as R506Q using the one­
letter code for an amino acid. Use of the three­letter code for an amino acid makes it much easier to identify the amino acid. For example, there are
multiple amino acids which start with the letter A, and therefore these amino acids must have different single letter codes for identification. It is not
clear, for example, why aspartic acid has a single letter amino acid code of D. Its three­letter code of Asp makes its identification much more obvious. A
protein variation is also written as p.R506Q, to indicate that the change is at the level of the amino acid sequence of the protein.

The next example describes a genetic variation in which a single nucleotide has been deleted from the gene for the cystic fibrosis transmembrane
regulator (CFTR). The colloquial name for this mutation is the Delta F508 mutation. At the genetic level, it is written as 1521_1523 del. This indicates that
the nucleotides from position 1521 up to 1523 are deleted. The nucleotides which are deleted may be mentioned, and in this case, the genetic variation
may be written as 1521_1523delCTT. The deletion of the nucleotide in the gene results in the deletion of the amino acid phenylalanine in the protein.
Therefore, the protein designation using the three­letter amino acid code is Phe508del.

There are many other variants that can be present in the genome. A duplication occurs when one or more nucleotides are duplicated. When the
nucleotides from position c.4375 to c.4385 are duplicated, the genetic variation is reported as c.4375_4385dup. When one or more nucleotides are
inserted into a gene, the sequence of three nucleotides in the gene is altered. As an example, c.4375_4376insACCT indicates that four nucleotides were
inserted between positions 4375 and 4376 in the gene. A number of more complex genetic variations are known to exist.

Clinical Studies—Tumor Genetics

When the DNA is extracted from non­tumor tissue of a patient, the genetic alterations described represent those found in the patient. However, DNA
can be also be extracted from samples of carefully collected tumor tissue, and the genetic alterations described in those evaluations most often
represent those found in the tumor tissue.

What follows is an example of a genetic variation found in many cancers in the BRAF gene. The BRAF­coded protein is part of a signaling pathway in
cells that controls a number of important cell functions. Somatic mutations (i.e., not present in the germ cells) in the BRAF gene are common in several
t f i l di l d f th l d t d th id l d Th lt f th t ti d h
cells that controls a number of important cell functions. Somatic mutations (i.e., not present in the germ cells) in the BRAF gene are common in several
types of cancers including melanoma, and cancers of the colon and rectum, ovary, and thyroid gland. The results of these mutations produce a change
in the signaling pathway in cells that leads to their uncontrolled growth. The mutation most commonly found in these cancers is one which replaces
the amino acid valine with the amino acid glutamic acid at position 600. This is written as Val600Glu or V600E. Laboratory reports will typically state the
presence or the absence of the BRAF mutation without description of the changes at the DNA or the protein level. Genetic information from tumors can
lead to important information about choice of chemotherapeutic agents and patient prognosis. It is now common to assess mutations in dozens of
different genes for a specific type of cancer. For example, a sample of breast cancer tissue can be analyzed to determine if there are genetic variations
in six genes, including the genes for hereditary breast cancer known as BRCA1/2. Another available combination includes 17 genes to be evaluated in
the assessment of treatment and prognosis for breast cancer patient. The analyses of these genes can involve targeted analysis for the presence of
specific genetic alterations or the sequencing of small or large segments within the gene.

Mutations in the BRAF gene, also known as the BRAF proto­oncogene, can also appear in a variety of nonmalignant conditions. For example, at least
two mutations in the BRAF gene have been found to cause Noonan syndrome. One change in the gene to produce Noonan syndrome results in
replacement of the amino acid threonine with the amino acid proline at position 241. This is written as Thr241Pro. There is another mutation in the
same gene which can also produce Noonan syndrome, and this variation is a replacement of the amino acid leucine with the amino acid phenylalanine
at position 245 written as Leu245Phe.

A liquid biopsy is an assessment using a blood sample for circulating tumor cells or segments of DNA from tumor cells. It can be used to detect cancer
early in the disease or to determine if a malignancy has recurred. Use of the blood samples rather than biopsies allows for more frequent evaluation of
the patient and the detection of new molecular changes that occur with progression of the disease.

Clinical Studies—Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS)

When a patient evaluation does not lead to a diagnosis but does suggest an underlying genetic cause, it is possible to sequence the whole exome or the
whole genome. This evaluation of the protein coding section of DNA sequences, that is WES, assesses only about 2 % of the DNA in human
chromosomes, but this analysis identifies many mutations associated with disease. A whole exome sequence provides data on thousands of genes.
WES can be performed on both tumor and non­tumor samples. The laboratory report from an exome analysis typically provides information on the
number of genetic alterations found. One section names the specific deleterious mutations in disease genes related to the clinical phenotype which is
submitted along with the sample. This genetic analysis would consider, for example, the presence of genetic variations associated with bleeding
syndromes in a patient with a bleeding disorder. Another section lists variations within disease­related genes which have unknown clinical significance
because it is not clear if the specific genetic variations are related to the clinical phenotype. Another section of the report lists mutations which are
medically actionable but unrelated to clinical phenotype, which is bleeding in this example. New associations between mutations and specific diseases
are appearing in the medical literature at a rapid rate. This has prompted the recommendation for whole exome and WGS (see below) that states
“perform it once, but analyze it frequently.”

The sequencing of both introns and exons, that is the whole genome, can also be performed. This analysis generates much more sequencing
information because it covers 95% to 98% of the entire genome, and can, therefore, identify mutations outside of exons. WGS is an option, as is exome
sequencing, when a diagnosis is elusive and it appears to have a genetic basis.

Currently, there is a debate over the benefits of WGS versus WES. The advantages of WES are largely less money and quicker turnaround time. WES
reads only approximately 2% of the genome so the cost of performing the test is less. There is also less required data storage, and faster and less
expensive data analyses. However, in WES, there are regions of the exome which are not sequenced, leading to missed identification of variants. The
use of WGS allows for better identification of a number of complex genetic alterations, such as copy number variations and rearrangements, which are
especially important in genetic analyses of tumors.

Clinical Studies—Pharmacogenomics

The terms pharmacogenomics and pharmacogenetics are often used interchangeably. Pharmacogenetics describes how a single gene variation
influences the response to a single drug. Pharmacogenomics is a broader term. In this description, the two terms will be used interchangeably.

It has long been known that some individuals do not respond as expected to certain medications. For many of these individuals, the explanation is that
a gene product associated with the metabolism of the drug causes the drug to be ineffective. In some cases, the gene codes for protein which
metabolizes a drug into an active form. An example of this situation is the gene CYP2C19 which codes for a protein that is an enzyme which metabolizes
h d l id li i i f h l id l b li i hibi l l h h h lf f h i b
metabolizes a drug into an active form. An example of this situation is the gene CYP2C19 which codes for a protein that is an enzyme which metabolizes
the drug clopidogrel into its active form. The clopidogrel metabolite inhibits platelets at the ADP receptor. When the normal form of the gene is absent,
it is known as a loss of function mutation because of the absence of the protein results in the patient being unable to generate the metabolite that is
the active drug. Different mutations in the CYP2C19 gene can produce a gain of function. In patients with these mutations, clopidogrel is transformed
more actively into its functional metabolite. In pharmacogenomics, the results are often but not always presented in the laboratory report as the allele,
that is, the form of the gene which is present. It is uncommon in pharmacogenomics to present the molecular alteration associated with an individual
allele. For example, a CYP2C19 allele known as *5 is associated with the replacement of a cytosine with a thymine at nucleotide position 1297 in the
CYP2C19 gene (1297C>T). This results in CYP2C19 protein in which amino acid 433 has a tryptophan in place of an arginine (Arg433Trp). Despite
knowledge of the change at the DNA level and at the protein level, the genetic description for this alteration is *X where the * indicates the allele which
is present. For the drug–gene interaction between clopidogrel and CYP2C19, there are multiple loss of function alleles and one well­recognized gain of
function allele. The normal allele, also called the wild–type allele for the CYP2C19 gene, is *1. All of the other alleles represent genetic variations leading
to loss of function or gain of function. Importantly, clopidogrel can be replaced by two other drugs which inhibit platelets at the ADP receptor.
Therefore, if a patient has a pharmacogenomic result that indicates an abnormal response to clopidogrel, the patient can receive a drug which is
equally effective, though more expensive, to produce the desired clinical effect.

Clinical Studies—Molecular Testing for Infectious Disease

Identification of infectious agents can be completed within hours using molecular testing. The evaluation does not require isolation of the agent and
growing it in culture, or testing it for a cytopathic effect, which can take days to weeks. Molecular­based techniques to determine if an infectious agent
is present often able to assess for multiple infectious agents in one assay. Such testing ultimately assesses the resemblance of the DNA segments
within the sample to known DNA sequences in microorganisms. The laboratory report indicates whether an agent of interest is detected or not. As an
example where a single agent is targeted, a test can indicate if Zika virus DNA is detected. For a gastrointestinal virus panel performed to identify any of
multiple agents causative for gastrointestinal illness, the laboratory report lists the agents which are detected.

CYTOGENETIC TESTING
Overview and Terminology

A karyotype allows for detection of gross alterations in chromosome size and in chromosome number. For example, cytogenetics allows for detection
of chromosome breakage and transfer when two chromosomes break and the fragments rejoin with different chromosomes. In a cytogenetics report,
the location of a gene on a chromosome is presented by first listing the number of the chromosome on which it is located, or the letter if it is on the X or
Y chromosome. Further localization is provided by the letter “p,” which indicates the shorter arm of the chromosome, or by the letter “q” which
indicates the longer arm of the chromosome. Further localization of a gene is provided by numbers that indicate first a region on the chromosome and
then the band stained in the cytogenetic preparation which is closest to the gene of interest. For example, “7q31” indicates that the gene of interest is
located on chromosome 7, on the long arm of the chromosome, within region 3, in band 1. Further information is provided by the terminology 7q31.1,
which indicates that the gene is in sub­band 1 within band 1. (See Chapter 2 for the methodology used in the karyotype analysis.)

Genetic Variations Identified by Cytogenetics

When genetic variations are a result of the movement of large segments of a chromosome, the changes may be observed by reviewing the appearance
of chromosomes in a karyotype analysis (see Chapter 2). A common variation visible by cytogenetics is a translocation. Translocations occur between
non­homologous chromosomes. These are chromosomes that contain different genes. Homologous chromosomes, by comparison, are the pair of
chromosomes, both of which have the same chromosome number, which are inherited as one from the mother and one from the father. Homologous
chromosomes have the same genes, though the alleles for the genes may be different. When a piece of DNA moves from chromosome A to
chromosome B, with no DNA from chromosome B transferring back to chromosome A, it is called a simple translocation. Alternatively, if a piece from
chromosome B transfers to chromosome A, it is called a reciprocal translocation. If the amount switched between two chromosomes is the same, the
translocation is balanced; and if the amount moving from one chromosome to another is larger than what is translocated back, the translocation is
unbalanced.

As an example, a piece of chromosome 8 breaks off and translocates to chromosome 14. In this example, the location on chromosome 8 where the
break occurred, is 8q24, and the location to which the piece is attached on chromosome 14 is 14q32. This translocation is reported as t(8;14)(q24;q32).
Many such translocations are described in Chapter 13 involving hematologic malignancies. Several types of cancer are caused by acquired
break occurred, is 8q24, and the location to which the piece is attached on chromosome 14 is 14q32. This translocation is reported as t(8;14)(q24;q32).
Many such translocations are described in Chapter 13 involving hematologic malignancies. Several types of cancer are caused by acquired
translocations. The “Philadelphia chromosome” found in chronic myelocytic leukemia is t(9;22)(q34;q11).

A translocation is only one of several cytogenetic changes. For example, pieces of chromosomes can be deleted. Deletion of a part of chromosome 5
which leads to cri­du­chat syndrome is reported as del(5). Extra chromosomes can arise. When a third chromosome of any type appears in a cell, the
condition is known as trisomy. Transposition is an event in which a piece of a single chromosome breaks off and reattaches to the same chromosome
in a different location. Crossing over occurs when genetic material is exchanged between homologous chromosomes during meiosis to produce
recombinant chromosomes. Inversion is an event in which a piece of a chromosome breaks off, turns upside down, and reinserts itself in the same
location. Duplication occurs when a piece of a chromosome is duplicated and remains present in the chromosome. There are other more complex
cytogenetic changes that are known to occur.

Clinical Studies—Fluorescence In Situ Hybridization (FISH)

FISH involves the use of fluorescent probes to detect and localize specific DNA sequences on the chromosomes. For example, FISH analysis can be
used to determine, using a probe for a gene on chromosome 21, the number of copies of chromosome number 21 which are present. Such an analysis
is informative in an evaluation for Down syndrome. Using probes for two separate genes, FISH analysis can be used to determine if the two genes of
interest are separated by a translocation or brought together by a translocation. FISH can also determine if a single gene has been disrupted by a
translocation. (See Chapter 2 for the methodology used in FISH analysis.)

Clinical Studies—Comparative Genomic Hybridization (CGH) and Array CGH

A laboratory evaluation related to FISH is CGH, and the newer array CGH is more sensitive and specific than conventional CGH. This analysis determines
whether there are gains or losses of either whole chromosomes or portions of a chromosome, and provides information on gene copy number
variation. The most frequently identified candidates for CGH testing are patients with cancer, patients who have mental retardation of unknown
etiology, and patients with congenital anomalies or dysmorphic features. (See Chapter 2 for the methodology used in CGH.)

FURTHER READING

den Dunnen JT, et al. HGVS recommendations for the description of sequence variants—2016 update. Hum Mutat . 2016;37:564–569. [PubMed:
26931183]

Committee on Diagnostic Error in Health Care. In: Balogh EP, Miller BT, Ball JR, eds. Improving Diagnosis in Health Care . Washington, DC: National
Academies Press; 2015:chap. 4.

Gornall AG. Basic concepts in laboratory investigation. In: Gornall AG, ed. Applied Biochemistry of Clinical Disorders . Philadelphia, PA: Harper and
Row; 1980:chap 1.

Laposata M, Dighe AS. “Pre­pre” and “post­post” analytical error: high incidence patient safety hazards involving the clinical laboratory. Clin Chem Lab
Med . 2007;45:712–719. [PubMed: 17579522]

Laposata ME, Laposata M, Van Cott EM, Buchner DS, Kashalo MS, Dighe AS. Physician survey of a laboratory medicine interpretative service and
evaluation of the influence of interpretations on laboratory test ordering. Arch Pathol Lab Med . 2004;128:1424–1427. [PubMed: 15578888]

McPherson RA. Laboratory statistics. In: McPherson RA, Pincus MR, eds. Henry's Clinical Diagnosis and Management by Laboratory Methods . 21st ed.
Philadelphia, PA: WB Saunders; 2006 [chapter 9].

Passiment E, Meisel JL, Fontanesi J, Fritsma G, Aleryani S, Marques M. Decoding laboratory test names: a major challenge to appropriate patient care.
J Gen Intern Med . 2013;28:453–458. [PubMed: 23192446]
Laposata's Laboratory Medicine: Diagnosis of Disease in the Clinical Laboratory, 3e

CHAPTER 2: Methods

Michael Laposata; James H. Nichols; Paul Steele; Thomas P. Stricker; Mayukh K. Sarkar

INTRODUCTION
No textbook in laboratory medicine would be complete without a description of methods used in the clinical laboratory. The methods described in this
chapter are predominantly the common ones found in clinical laboratories. Each method description provides an overview of the basic concept of the
assay, minimizing the details, while including clinically important information and a comment on the expense of the test and the complexity of the
assay in the laboratory.

Some methods describe specific assays used almost exclusively in the clinical laboratory. For example, the PT and PTT are tests used for clinical
assessment, with the goal to identify factor deficiencies in the coagulation cascade. Other methods are standard techniques used inside and outside
the clinical laboratory. As an example, flow cytometry is a standard technique used in a variety of settings, and in this chapter it is shown how it is used
in clinical laboratory testing.

Some tests are performed outside the laboratory in the vicinity of the patient. These tests are called “point­of­care tests,” commonly abbreviated as
POCT. This section contains illustrations for point­of­care testing for glucose and for point­of­care testing for a variety of compounds that can be
detected by immunological methods (immunoassays).

There is rapid growth of testing in the clinical laboratory for genetic alterations. These laboratory studies are often highly complex and very expensive,
and it is difficult for most clinical laboratories to perform them for these reasons. In addition, the clinical impact of many genetic alterations remains
unknown. Therefore, it is not uncommon for a genetic test, especially an assay involving gene sequencing, to produce results that have no known
clinical significance. Selected genetic methods for detection of mutations and for gene sequencing are illustrated in this chapter.

The expense assessment attached to each assay described in this chapter is an approximation, listed as low, moderate, or high. It should be
understood that the charge for the test set by the institution operating the laboratory is usually proportional to the expense of the reagents, supplies,
and labor required to perform the test. On occasion, however, there is a great disparity between the actual expense to perform the test and the amount
charged by the institution for the assay. With this in mind, the expense estimation provided for each method in this chapter is more closely related to
the actual cost of reagents, supplies, and labor in the laboratory, with the understanding that the amount charged for the test should be in the same
range of low, moderate, or high—but it is not always the case.

Each method also has a descriptor to reflect whether it is manual, semiautomated, or highly automated. A comment has been added if microscopy is
involved, as this makes any technique highly manual. It should be noted that for some methods, there is an option for manual performance or for
using some level of automation. Manual methods are often less expensive. There is usually greater automation in the larger clinical laboratories
because larger laboratories are more likely to have the test volume and the financial resources to justify the automated option. The term
“semiautomated” indicates that there is a manual component associated with the use of an instrument that performs some steps of the analysis.

The turnaround time for an assay is not provided because it is impossible to know all of the elements associated with the turnaround time for a test
within an individual institution. Broadly speaking, turnaround time is shorter for assays that are highly automated and less expensive, and longer for
assays that are manual and highly expensive. It is important to understand that the turnaround time for an assay can be calculated using different
starting points. For example, one starting point is the time a sample is collected. Another starting point is the time that a sample enters the laboratory.
However, the most relevant starting time clinically, which predates the previous two starting times, is the time at which the physician orders the test.
Similarly, there are different end points in the assessment of turnaround time. Most commonly, the end point is the time at which the result is reported
by the laboratory into the laboratory information system. However, it is most important to know when the physician becomes aware of the result. This
end point is extremely difficult to ascertain, and, therefore, virtually always the end point is considered to be the time at which the result is reported by
the laboratory.
end point is extremely difficult to ascertain, and, therefore, virtually always the end point is considered to be the time at which the result is reported by
the laboratory.

Broadly speaking, the turnaround time is shorter for assays that are highly automated and less expensive, and longer for assays
that are manual and highly expensive.

Finally, it should be noted what methods are not presented in this chapter. There are a number of methods that have been used progressively less over
time, and in many institutions these assays are no longer performed at all in the clinical laboratory. These are numerous and include the
radioimmunoassay (RIA), immunoelectrophoresis, lipoprotein electrophoresis, and the bleeding time. Also less frequently performed assays are not
described in this chapter. Though this number of the infrequently used methods may be large, the number of tests performed using these methods
account for a small percentage of the total tests performed in a typical hospital clinical laboratory.

METHODS IN CLINICAL IMMUNOLOGY


Antinuclear antibody (ANA) testing

FIGURE 2–1

Protein electrophoresis (PEP)

FIGURE 2–2
Immunofixation to identify monoclonal immunoglobulins

FIGURE 2–3
Flow cytometry

FIGURE 2–4
Nephelometry

FIGURE 2–5
Cryoglobulin analysis

FIGURE 2–6

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