Milford Molecular Diagnostics

2044 Bridgeport Ave, Milford, CT 06460

 


Milford Molecular Diagnostics


"DNA sequencing-based diagnostics are our specialty and routine diagnostic DNA sequencing is the gateway to practicing personalized molecular medicine."


Sin Hang Lee, MD, F.R.C.P.(C), FCAP



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Frequently Asked Questions
Lyme Disease Testing

Do patients with “chronic Lyme disease” still harbor Lyme bacteria in the body?

 

We do not know the answer to this question. Many experts say that the patients suffering from chronic symptoms and found to have Lyme bacteria in the blood or body fluids are due to new infections, not a result of lingering old infections.

Our task is to answer the question: Can we find “Lyme disease bacteria”, dead or alive, in the patient’s specimen submitted for testing? We will provide the best evidence-based answer to the treating physician for patient management. Only the physician of a patient can decide if the findings of pathogenic spirochetes represent a new infection or the residues of an earlier infection. However, even if we cannot find  the pathogens, the negative test result does not mean there are no Lyme bacteria in the patient’s body.

 

How can someone who suspects that he or she might have Lyme disease, use our DNA sequencing services?

 

Milford Molecular Diagnostics is licensed by the State of Connecticut Department of Public Health to perform DNA sequencing-based tests for Lyme borrelioses [1, 2], human papillomavirus infection and genotyping [5-9], Chlamydia trachomatis infection [10,11] and Neisseria gonorrhoeae infection [10, 11].


Our tests for Lyme borrelioses are designed to detect the infectious agents, namely the spirochetes that cause Lyme disease and Lyme disease-like borrelioses in the blood, in the cerebrospinal fluid (CSF), and in the joint fluid. A medical doctor or an equally qualified health care provider is the best person to determine if and when the patient may have the spirochete bacteria in the blood (spirochetemia), in the CSF, or in the joint (synovial) fluid.


Patients with Lyme disease or Lyme disease-like borrelial infections do not always have the infectious agents in these body fluids. It is wasting health care resources to test a sample which is unlikely to have pathogenic borrelial bacteria in it even if the patient does have the disease because the spirochetes may be hiding in the deep tissues, and are not in the body fluids. The patient and the treating physician can decide when is the best time to draw blood samples for the testing--probably when the patient is having some unexplained flu-like symptoms in the summer when it is not a flu season.


However, the spirochetes will not stay in the blood of the patient for long because they prefer to live in the deep tissues, such as the joints, the heart and the nervous system. The window of opportunity to find the spirochetes in the blood is narrow, and varies from individual to individual. A correct and timely diagnosis of Lyme disease is usually initiated by an informed patient living in a disease-endemic area who will seek medical advice without delay when the clinical symptoms are developing while the spirochetes are travelling through the blood from one organ to another. The clinical symptoms may subside spontaneously without treatment after the spirochetes have disappeared from the circulating blood only to invade the deep tissues.

 

How can you, as a patient, order a DNA sequencing test?

 
If you and your health care provider suspect that you may have Lyme disease or Lyme disease–like borreliae in your blood, joint (synovial) fluid or cerebrospinal fluid (CSF), you may send a specimen, a requisition form (see our Request a Test page) signed by your health care provider and a check for $150.00 made payable to "Milford Molecular Diagnostics" via Federal Express overnight delivery to:


Milford Molecular Diagnostics

2044 Bridgeport Avenue

Milford, CT 06460 


Acceptable specimens are:

1.)  3 mL venous blood collected in a lavender-top test tube containing EDTA as anticoagulant if spirochetemia is suspected

2.)  1.0-2.0 mL synovial fluid in a plastic, leak-proof container (a sterile vial or a tube with screw cap) if Lyme arthritis is suspected

3.)  1.0-2.0 mL CSF in a plastic, leak-proof container (a sterile vial or a tube with screw cap) if neuroborreliosis is suspected

 
Serum samples and plasma prepared by high speed centrifugation for routine chemistry tests are not suitable for detection of infectious agents of Lyme disease or related borrelioses. For mailing requirements, please consult the following Federal Express (FedEx) Packaging Guidelines for Clinical Samples document. Please schedule sample shipping so that they are delivered to Milford Molecular Diagnostics Monday through Friday. Samples cannot be received on Saturday or Sunday.

 
Our official laboratory report will be sent, within 5 to 7 working days after receipt of the specimen, to the patient’s health care provider listed on the requisition form for proper clinical follow-up. A base-calling DNA sequencing electropherogram with its GenBank BLAST alignment analysis will accompany the report if the test result is positive.

 

My doctor thought I had an active Lyme disease infection when my blood sample was drawn for testing. Why did your laboratory test on this sample turn out to be negative for spirochetemia?

 
A laboratory test result is only one piece of information used by a treating physician--who is the best person to make the diagnosis of Lyme disease. Lyme disease spirochetemia is similar to the septicemia in typhoid and paratyphoid fever except that the spirochetes hardly multiply in the circulating blood. For Salmonella, the bacteria causing typhoid fever, one bacterium in a 10 mL of blood sample can give rise to a positive culture because Salmonella, unlike Lyme disease bacteria can grow easily and rapidly in artificial culture media. Even for the diagnosis of typhoid fever, a single blood culture is positive in only half of cases, according to the CDC guidelines. We do not know how many spirochetes of B. burgdoreri or B. miyamotoi in a patient’s blood sample are needed to generate a positive culture result because no research has been done along this line. In using our PCR/DNA sequencing technology to test for Lyme and related borrelioses, the limit of detection is 25 bacteria per mL of blood. However, we do not know if the level of bacterial density is correlated with the severity of a patient's symptoms as observed by their treating physician.

 

How can you order a DNA sequencing test for Lyme disease bacteria on ticks?

 

Many patients and their health care providers want to know if the ticks removed from skin bites are infected with Borrelia burgdorferi or Borrelia miyamotoi. For tick testing, you do not need a signature from a licensed health care provider. All you need is to put the carcass of the tick removed from skin in a small plastic bag with a zip-lock seal, a requisition form (see our Request a Test page) and a check for $75.00 made payable to "Milford Molecular Diagnostics" in an envelope and mail by first class mail via the USPS to:


Milford Molecular Diagnostics

2044 Bridgeport Avenue

Milford, CT 06460 


Our official laboratory report will be sent to the client at the address written on the order form. A base-calling DNA sequencing electropherogram with its GenBank BLAST alignment analysis will accompany the report if the test result is positive.

 

My doctor thinks I might have Lyme disease; however, not yet convincingly diagnosed. I do not currently have symptoms of spirochetemia. When I did have flu-like symptoms, the result of my serology test was questionable for Lyme disease. Can you test the archived serum sample leftover to see if there are Lyme disease bacteria in it?

 
Serum is a very poor sample for routine detection of Lyme disease bacteria because most of the spirochetes in the blood are trapped in the blood clot and lost in high-speed centrifugation during preparation of the serum sample for serology tests. Furthermore, serum samples are not stored in sterile containers, and are subject to contamination by environmental bacteria and fungi.


However, some serum samples of Lyme borreliosis patients, if stored properly, do contain residual “Lyme disease” bacteria that can be detected by our highly sensitive nested PCR/DNA sequencing technology, as shown in Case 1 and Case 2 of our DNA Sequence Testing page.


If you and your treating physician feel strongly that it is worthwhile testing an archived serum sample for Lyme borreliae, please contact us for special arrangements because the serum sample must be sent in a thermo-insulated container with dry ice to avoid contaminant overgrowth during transit. The fee to test for Lyme disease borreliae in an archived serum sample is $450.00 because multiple PCR tubes must be set up for DNA amplification in order to increase the chance of detection.

 

References
 

  1. Lee SH, Vigliotti VS, Vigliotti JS, Jones W, Pappu S. Increased Sensitivity and Specificity of Borrelia burgdorferi 16S Ribosomal DNA Detection.  Am J Clin Path. 2010;133:569-576.
  2. Lee SH, Vigliotti VS, Vigliotti JS, Jones W, Williams J, Walshon J. Early Lyme disease with spirochetemia – diagnosed by DNA sequencing. BMC Res Notes. 2010;3:273.
  3. http://www.cdc.gov/ticks/miyamotoi.html
  4. Hong G, Lee SH, Ge S, Zhou S. A Novel Low Temperature PCR Assured High-Fidelity DNA Amplification. International Journal of Molecular Sciences. 2013; 14(6):12853-12862.
  5. Lee SH, Vigliotti VS, Vigliotti JS, Pappu S. Routine human papillomavirus genotyping by DNA sequencing in community hospital laboratories. Infect Agent Cancer 2007; 2:11.
  6. Lee SH, Vigliotti VS, Pappu S. Human papillomavirus (HPV) infection among women in a representative rural and suburban population of the United States. Inter J Gyn Ob.  2009; 105:210-214.
  7. Lee SH,  Pappu S. Validation of human papillomavirus genotyping by signature DNA sequence analysis. BMC Clin Pathol  2009; 9:3.
  8. Lee SH, Pappu S. Signature sequence validation of human papillomavirus type 16 (HPV-16) in clinical specimens. J Clin Path. 2010;63:235-239.
  9. Lee SH: Chapter 5 in “Guidelines for the use of molecular tests for the detection and genotyping of human papilloma virus from clinical specimens.” Methods Mol Biol 2012; 903:65-101.
  10. Lee SH, Vigliotti VS, Pappu S. DNA Sequencing Validation of Chlamydia trachomatis and Neisseria gonorrhoeae Nucleic Acid Tests. Am J Clin Pathol. 2008;129:852-859.
  11. Lee SH, Vigliotti VS, Pappu S. Molecular tests for human papillomavirus (HPV), Chlamydia trachomatis and Neisseria gonorrhoeae in liquid-based cytology specimen.  BMC Women’s Health 2009; 9:8.
Women's Healthcare Sequencing Tests

Why nested PCR/Sanger sequencing?

 

Nested PCR (polymerase chain reaction) increases the sensitivity of DNA detection 10 to 100 times by performing PCR amplification of the target DNA twice consecutively in tandem. Sanger sequencing is the gold standard for all DNA-based tests and nucleic acid researches. We combine these two technologies to ensure high sensitivity and specificity of these molecular tests to further improve the quality of women’s health care. For example, the practice of using HPV assay instead of Pap cytology to assess cervical cancer risk is based on the original study of the relationship between HPV persistent infection and cervical cancer by the nested PCR and Sanger sequencing HPV genotyping technologies [1]. The current commercial HPV tests without nested PCR and Sanger sequencing may generate up to 40% errors according to one New York State Department of Health proficiency survey analysis [2]. Such errors may lead to unnecessary colposcopic cervical biopsies or failure to detect CIN3 lesions or cervical cancers.

 

Is BRCA 1 and 2 founder gene mutations screen cost-effective?

 

In the general population, about 5 to 10% of breast cancers are inherited, and most of these are due to detectable mutations in the BRCA1 and BRCA2 genes; up to 14% of ovarian cancers are hereditary; but over 99% of women do not have detectable BRCA 1 and 2 gene mutations [3].

Various mutations of BRCA1 and 2 in different ethnic populations have been described, most with questionable significance. However, the BRCA1 and BRCA2 founder gene mutation carriers have an estimated 56–84% lifetime risk of developing breast cancer. For ovarian cancer, BRCA1 is associated with a 36–63% lifetime risk as opposed to 10–27% for BRCA2 carriers [4]. About 2.5% of Ashkenazi Jews carry one of the three founder gene mutations, namely the BRCA1 185delAG, BRCA1 5382insC, or BRCA2 6174delT [5]. Studies have shown that these three founder mutations represent 95% of all BRCA1 and BRCA2 mutations identified in this population via DNA sequence analysis [6]. The College of American Pathologists (CAP) and the American College of Medical Genetics (ACMG) now only oversee the proficiency testing program on these three founder mutations for BRCA testing regulation [7].

 

Why not do full-length sequencing of the genes?

 
In the general population, the overall prevalence of BRCA1 founder mutations is estimated at 1 in 300 and that of BRCA2 founder mutation is estimated at 1 in 800 [8]. If full-length sequencing of the genes is performed for mutation screen, between 10% and 15% of individuals undergoing genetic testing for BRCA1 and BRCA2 mutations will be found to have a variant of uncertain significance (VUS). VUSs are even more common in non-white populations, with frequencies as high as 46% in African Americans and 22% in Hispanics [9].  Therefore, experts in the field have recommended that BRCA1 and BRCA2 testing focuses solely on unambiguously loss-of-function mutations with definitive effect on cancer risk [10].

 
Why do we need sequencing Chlamydia trachomatis and Neisseria Gonorrhoeae tests?

 
Commercial test kits may generate false positive results. They were developed in high-prevalence populations where a few percentages of false-positive test results are tolerable. For low-prevalence populations, the Centers for Disease Control and Prevention (CDC) recommends that an additional test with a different method or with the same method be performed to confirm a positive nucleic acid test result for C trachomatis or for N gonorrhoeae to reduce the possibility of false-positive results that may have adverse medical, social, and psychological impacts on the patient [11]. DNA sequencing analysis test provides no false-positive diagnosis [12].


References

 

  1. Wallin KL, Wiklund F, Angström T, Bergman F, Stendahl U, Wadell G, Hallmans G, Dillner J. Type-specific persistence of human papillomavirus DNA before the development of invasive cervical cancer. N Engl J Med. 1999;341:1633-8.
  2. Lee SH, Zhou S, Zhou T, Hong G. Sanger Sequencing for BRCA1 c.68_69del, BRCA1 c.5266dup and BRCA2 c.5946del Mutation Screen on Pap Smear Cytology Samples. Int J Mol Sci. 2016; 17(2):229.
  3. Department of Public Health, State of Connecticut.  Breast Cancer: Genetic Testing for Hereditary Breast & Ovarian Cancer: What You Should Know. http://www.ct.gov/dph/cwp/view.asp?a=3134&q=396624
  4. Finkelman BS, Rubinstein WS, Friedman S, et al. Breast and ovarian cancer risk and risk reduction in Jewish BRCA1/2 mutation carriers. J Clin Oncol 2012;30:1321–8.
  5. Roa BB, Boyd AA, Volcik K, Richards CS. Ashkenazi Jewish population frequencies for common mutations in BRCA1 and BRCA2. Nat Genet 1996;14:185–7.
  6. Phelan CM, Kwan E, Jack E, et al. A low frequency of non-founder BRCA1 mutations in Ashkenazi Jewish breast-ovarian cancer families. Hum Mutat 2002;20:352–7.
  7. Tafe, L.J.; Datto, M.B.; Palomaki, G.E.; Lacbawan, F.L.; CAP/ACMG Biochemical and Molecular Genetics Resource Committee. Molecular testing for the BRCA1 and BRCA2 Ashkenazi Jewish founder mutations: A report on the College of American Pathologists proficiency testing surveys. Genet. Med. 2015; 17: 58–62.
  8. Hampel H, Bennett RL, Buchanan A, Pearlman R, Wiesner GL; Guideline Development Group, American College of Medical Genetics and Genomics Professional Practice and Guidelines Committee and National Society of Genetic Counselors Practice Guidelines Committee.. A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. Genet Med. 2015;17:70-87.
  9. Domchek S, Weber BL. Genetic variants of uncertain significance: Flies in the ointment. J Clin Oncol. 2008; 26: 16–7.
  10. King MC, Levy-Lahad E, Lahad A. Population-based screening for BRCA1 and BRCA2: 2014 Lasker Award. JAMA 2014; 312: 1091–2.
  11. Centers for Disease Control and Prevention. Screening tests to detect Chlamydia trachomatis and Neisseria gonorrhoeae infections, 2002. MMWR Morb Mortal Wkly Rep. 2002;51(RR15):1-27.
  12. Lee SH, Vigliotti VS, Pappu S. DNA sequencing validation of Chlamydia trachomatis and Neisseria gonorrhoeae nucleic acid tests. Am J Clin Pathol. 2008 Jun;129(6):852-9.