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MP 2.04.83 Genetic Testing for FMR1 mutations (including Fragile X Syndrome)

Medical Policy    
Section
Medicine 
Original Policy Date
 June 2012
Last Review Status/Date
Reviewed with literature search/6:2014
Issue
6:2014
  Return to Medical Policy Index

Disclaimer

Our medical policies are designed for informational purposes only and are not an authorization, or an explanation of benefits, or a contract.  Receipt of benefits is subject to satisfaction of all terms and conditions of the coverage.  Medical technology is constantly changing, and we reserve the right to review and update our policies periodically. 


Description

Fragile X syndrome (FXS) is the most common inherited form of mental disability and known genetic cause of autism. The diagnosis includes use of a genetic test that determines the number of CGG repeats in the fragile X gene.

Background

Fragile X Syndrome

FXS is the most common cause of heritable intellectual disability, characterized by moderate intellectual disability in males and mild intellectual disability in females. FXS affects approximately 1 in 4000 males and 1 in 8000 females. In addition to intellectual impairment, patients present with typical facial features, such as an elongated face with prominent forehead, protruding jaw, and large ears. Connective tissue anomalies include hyperextensible finger and thumb joints, hand calluses, velvet-like skin, flat feet, and mitral valve prolapse. The characteristic appearance of adult males includes macroorchidism. Patients may show behavioral problems including autism spectrum disorders, sleeping problems, social anxiety, poor eye contact, mood disorders, and hand-flapping or biting. Another prominent feature of the disorder is neuronal hyperexcitability, manifested by hyperactivity, increased sensitivity to sensory stimuli, and a high incidence of epileptic seizures.

Approximately 1% to 3% of children initially diagnosed with autism are shown to have FXS, with expansion of the CGG trinucleotide repeat in the FMR1 gene to full mutation size of 200 or more repeats.(1) A considerable number of children evaluated for autism have been found to have FMR1 premutations (55-200 CGG repeats).(2) In one author’s experience, 2% of persons ascertained through a dedicated autism clinic had either an FMR1 full mutation or premutation.

Treatment of FXS

Current approaches to therapy are supportive and symptom-based. Psychopharmacologic intervention to modify behavioral problems in a child with FXS may represent an important adjunctive therapy when combined with other supportive strategies including speech therapy, occupational therapy, and special educational services. Medication management may be indicated to modify attention deficits, impaired impulse control, and hyperactivity. Anxiety-related symptoms, including obsessive-compulsive tendencies with perseverative behaviors, also may be present and require medical intervention. Emotional lability and episodes of aggression and self-injury may be a danger to the child and others around him or her; therefore, the use of medication(s) to modify these symptoms also may significantly improve an affected child’s ability to participate more successfully in activities in home and school settings.

Genetics of FXS

FXS is associated with the expansion of the CGG trinucleotide repeat in the fragile X mental retardation 1 (FMR1) gene on the X chromosome. Diagnosis of FXS may include using a genetic test that determines the number of CGG repeats in the fragile X gene. The patient is classified as normal, intermediate (or “gray zone”), permutation, or full mutation based on the number of CGG repeats(3):

  • Full mutation: >200-230 CGG repeats (methylated)
  • Premutation: 55-200 CGG repeats (unmethylated)
  • Intermediate: 45-54 CGG repeats (unmethylated)
  • Normal: 5-44 CGG repeats (unmethylated)

Full mutations are associated with FXS, which is caused by expansion of the FMR1 gene CGG triplet repeat above 200 units in the 5’ untranslated region of FMR1, leading to hypermethylation of the promoter region followed by transcriptional inactivation of the gene. FXS is caused by a loss of the fragile X mental retardation protein (FMRP).

Patients with a premutation are carriers and may develop an FMR1-related disorder, such as fragile X-associated tremor/ ataxia syndrome (FXTAS) or, in women, fragile X-associated premature ovarian insufficiency (FXPOI). FXTAS is a late-onset syndrome, comprising progressive development of intention tremor and ataxia, often accompanied by progressive cognitive and behavioral difficulties, including memory loss, anxiety, reclusive behavior, deficits of executive function, and dementia.

Premutation alleles in females are unstable and may expand to full mutations in offspring. Premutations of fewer than 59 repeats have not been reported to expand to a full mutation in a single generation. Premutation alleles in males may expand or contract by several repeats with transmission; however, expansion to full mutations has not been reported.

Premutation allele prevalence in whites is approximately 1 in 1000 males and 1 in 350 females.(3-5) Full mutations are typically maternally transmitted. The mother of a child with an FMR1 mutation is almost always a carrier of a premutation or full mutation. Women with a premutation are at risk of premature ovarian insufficiency and at small risk of FXTAS; they carry a 50% risk of transmitting an abnormal gene, which contains either a premutation copy number (55-200) or a full mutation (>200) in each pregnancy.

Men who are premutation carriers are referred to as transmitting males. All of their daughters will inherit a premutation, but their sons will not inherit the premutation. Males with a full mutation usually have intellectual disability and decreased fertility.

FDA Status

No U.S. Food and Drug Administration-cleared genotyping tests were found. Thus, genotyping is offered as a laboratory-developed test. Clinical laboratories may develop and validate tests in-house (“home-brew”) and market them as a laboratory service; such tests must meet the general regulatory standards of the Clinical Laboratory Improvement Act (CLIA). The laboratory offering the service must be licensed by CLIA for high-complexity testing.

Asuragen offers the Xpansion Interpreter™ test, which analyzes AGG sequences that interrupt CGG repeats and may stabilize alleles, protecting against expansion in subsequent generations.(6, 7)


Policy 

Genetic testing for FMR1 mutations may be considered medically necessary for the following patient populations:

  • Individuals of either sex with intellectual disability, developmental delay, or autism spectrum disorder (see Policy Guidelines section*).
  • Individuals seeking reproductive counseling who have a family history of fragile X syndrome or a family history of undiagnosed intellectual disability (see Policy Guidelines section*).
  • Prenatal testing of fetuses of known carrier mothers (see Policy Guidelines section*).
  • Affected individuals or relatives of affected individuals who have had a positive cytogenetic fragile X test result who are seeking further counseling related to the risk of carrier status (see Policy Guidelines section**).

Genetic testing for FMR1 mutations is investigational for all other uses.


Policy Guidelines

* According to the American College of Medical Genetics (ACMG), the following is the preferred approach to testing:

  • DNA analysis is the method of choice if one is testing specifically for fragile X syndrome and associated trinucleotide repeat expansion in the FMR1 gene.
  • For isolated cognitive impairment, DNA analysis for fragile X syndrome should be performed as part of a comprehensive genetic evaluation that includes routine cytogenetic evaluation. Cytogenetic evaluation is important in these circumstances because constitutional chromosome abnormalities have been identified as frequently as or more frequently than fragile X mutations in mentally retarded patients referred for fragile X testing.
  • Fragile X testing is not routinely warranted for children with isolated attention-deficit/hyperactivity.(8)
  • For individuals who are at risk due to an established family history of fragile X syndrome, DNA testing alone is sufficient. If the diagnosis of the affected relative was based on previous cytogenetic testing for fragile X syndrome, at least 1 affected relative should have DNA testing.
  • Prenatal testing of a fetus should be offered when the mother is a known carrier to determine whether the fetus inherited the normal or mutant FMR1 gene. Ideally DNA testing should be performed on cultured amniocytes obtained by amniocentesis after 15 weeks’ gestation. DNA testing can be performed on chorionic villi obtained by chorionic villus sampling at 10 to 12 weeks’ gestation, but results must be interpreted with caution because the methylation status of the FMR1 gene is often not yet established in chorionic villi at the time of sampling. Follow-up amniocentesis may be necessary to resolve an ambiguous result.
  • If a woman has ovarian failure before the age of 40, DNA testing for premutation size alleles should be considered as part of an infertility evaluation and before in vitro fertilization.
  • If a patient has cerebellar ataxia and intentional tremor, DNA testing for premutation size alleles, especially among men, should be considered as part of the diagnostic evaluation.

** This is due to the fact that cytogenetic testing was used before the identification of the FMR1 gene and is significantly less accurate than the current DNA test. DNA testing would accurately identify premutation carriers and distinguish premutation from full mutation carrier women.(9)

The ACMG Professional Practice and Guidelines Committee made recommendations regarding diagnostic and carrier testing for fragile X syndrome to provide general guidelines to aid clinicians in making referrals for testing the repeat region of the FMR1 gene. These recommendations include testing of individuals of either sex who have intellectual disability, developmental delay, or autism, especially if they have any physical or behavioral characteristics of fragile X syndrome.(9)

Physical and behavioral characteristics of fragile X syndrome include: typical facial features, such as an elongated face with prominent forehead, protruding jaw, and large ears. Connective tissue anomalies include hyperextensible finger and thumb joints, hand calluses, velvet-like skin, flat feet, and mitral valve prolapse. The characteristic appearance of adult males includes macroorchidism. Patients may show behavioral problems including autism spectrum disorders, sleeping problems, social anxiety, poor eye contact, mood disorders, and hand-flapping or biting. Another prominent feature of the disorder is neuronal hyperexcitability, manifested by hyperactivity, increased sensitivity to sensory stimuli, and a high incidence of epileptic seizures.

Coding

Effective in 2012, there are specific CPT codes for this testing:

81243: FMR1 (Fragile X mental retardation 1) (eg, fragile X mental retardation) gene analysis; evaluation to detect abnormal (eg, expanded) alleles

81244: FMR1 (Fragile X mental retardation 1) (eg, fragile X mental retardation) gene analysis; characterization of alleles (eg, expanded size and methylation status)


Benefit Application
BlueCard/National Account Issues

No applicable information 


Rationale

Literature Review

This policy was created in 2012 and is based on a search of the MEDLINE database through May 31, 2014. Literature that describes the analytic validity, clinical validity, and clinical utility of genetic testing for Fragile X syndrome (FXS) was sought.

Analytic Validity/Clinical Validity

Analytic validity refers to the technical accuracy of the test in detecting a mutation that is present or in excluding a mutation that is absent. Clinical validity refers to the diagnostic performance of the test (sensitivity, specificity, positive and negative predictive values) in detecting clinical disease.

For FXS, analytic and clinical validity are the same because the diagnosis of FXS is based on detection of an alteration in the FMR1 gene.

According to a large reference laboratory, analytic sensitivity and specificity of FMR1 screen with reflex to FMR1 diagnostic, FMR1 diagnostic, and FMR1 fetal diagnostic, is 99%.(10,11) Clinical sensitivity and specificity is 99% for premutation and full mutation alleles. Diagnostic errors can occur due to rare sequence variations.

DNA studies are used to test for FXS. Genotypes of individuals with symptoms of FXS and individuals at risk for carrying the mutation can be determined by examining the size of the trinucleotide repeat segment and methylation status of the FMR1 gene. Two main approaches are used: polymerase chain reaction (PCR) and Southern blot analysis.

The difficulty in fragile X testing is that the high fraction of GC bases in the repeat region makes it extremely difficult for standard PCR techniques to amplify beyond 100 to 150 CGG repeats. Consequently, Southern blot analysis is commonly used to determine the number of triplet repeats in FXS and methylation status.

PCR analysis utilizes flanking primers to amplify a fragment of DNA spanning the repeat region. Thus, the sizes of PCR products are indicative of the approximate number of repeats present in each allele of the individual being tested. The efficiency of the PCR reaction is inversely related to the number of CGG repeats, so large mutations are more difficult to amplify and may fail to yield a detectable product in the PCR assay. This, and the fact that no information is obtained about FMR1 methylation status, are limitations of the PCR approach. On the other hand, PCR analysis permits accurate sizing of alleles in the normal zone, the “gray zone,” and premutation range on small amounts of DNA in a relatively short turnaround time. Also, the assay is not affected by skewed X-chromosome inactivation.(3,9)

Unlike PCR, Southern blotting is time-consuming and requires large amounts of DNA. Alternatives to Southern blotting for determining FMR1 methylation status are in development. These include methylation-sensitive PCR and methylation-specific melting curve analysis.(12-15)

Quality assessment schemes have shown wide disparity in allele sizing between laboratories.(16) Therefore, in 2011, a panel of genotyping reference materials for FXS syndrome was developed and is expected to be stable over many years and available to all diagnostic laboratories. A panel of 5 genomic DNA samples was endorsed by the European Society of Human Genetics and approved as an International Standard by the Expert Committee on Biological Standardization at the World Health Organization. Patient blood samples were collected from 6 consenting donors; 1 donor was a normal female, and the remainder had been identified after previous molecular genetic investigation. Classifications of these patients were: female premutation, male premutation, male full mutation, and female full mutation. In all, 38 laboratories were invited to take part in the study, 23 laboratories agreed to participate, and results were returned by 21 laboratories. The participating 21 laboratories evaluated the samples (blinded, in triplicate) using their routine methods alongside in-house and commercial controls. Seventeen countries were represented among participating laboratories: 13 from Europe, 4 from North America, 3 from Australasia, and 1 from Asia. Collaborative validation study participants were requested to test 18 coded samples on 3 separate days using different lots of reagents or different operators if possible. A total of 18 nonconsensus results were reported, giving an overall rate of nonconcordance of 4.9% (21 laboratories ´ 18 samples – 7 samples not tested), although these were clustered in 3 laboratories. There was no correlation between nonconcordant results and any particular sample or a specific method. One laboratory reported 12 of the 18 nonconcordant results. This laboratory was contacted, and their testing protocol was changed.

CGG-repeat expansion full mutations account for more than 99% of cases of FXS.(9) Therefore, tests that effectively detect and measure the CGG repeat region of the FMR1 gene are more than 99% sensitive. Positive results are 100% specific. There are no known forms of fragile X mental retardation protein (FMRP) deficiency that do not map to the FMR1 gene.

Clinical Utility

Refers to how the results of the diagnostic test will be used to change patient management and whether these changes in management lead to clinically important improvements in health outcomes.

Evidence on the clinical benefit of testing for FXS is largely anecdotal. Clinical utility of genetic testing can be considered in the following clinical situations: (1) individuals with a clinical diagnosis of intellectual disability, developmental delay, or autism, especially if they have any physical or behavioral characteristics of FXS, a family history of FXS, or male or female relatives with undiagnosed intellectual disability, and (2) individuals seeking reproductive counseling.

Clinical utility for these patients depends on the ability of genetic testing to make a definitive diagnosis and for that diagnosis to lead to management changes that improve outcomes. No studies were identified that described how a molecular diagnosis of FXS changed patient management. Therefore there is no direct evidence for clinical utility of genetic testing in these patients.

Because there is no specific treatment for FXS, making a definitive diagnosis will not lead to treatment that alters the natural history of the disorder. There are several potential ways in which adjunctive management might be changed after confirmation of the diagnosis by genetic testing. The American Academy of Pediatrics (AAP)(5) and the American Academy of Neurology (AAN)(17) recommend cytogenetic evaluation in individuals with developmental delay to look for certain chromosomal abnormalities that may be causally related to their condition. AAN guidelines note that only in occasional cases will an etiologic diagnosis lead to specific therapy that improves outcomes but suggest more immediate and general clinical benefits of achieving a specific genetic diagnosis from the clinical viewpoint, as follows:

  • limit additional diagnostic testing;
  • anticipate and manage associated medical and behavioral comorbidities;
  • improve understanding of treatment and prognosis; and
  • allow counseling regarding risk of recurrence in future offspring and help with reproductive planning.

AAP and AAN guidelines also emphasize the importance of early diagnosis and intervention in an attempt to ameliorate or improve behavioral and cognitive outcomes over time.

Hersh et al (2011) reported on families with an affected male and whether an early diagnosis would have influenced their reproductive decision making.(5) After a diagnosis in the affected male was made, 73% of families reported that the diagnosis of FXS affected their decision to have another child, and 43% of the families surveyed had had a second child with a full mutation.

Testing the repeat region of the FMR1 gene in the context of reproductive decision making may include testing individuals with either a family history of FXS or a family history of undiagnosed intellectual disability, fetuses of known carrier mothers, or affected individuals or their relatives who have had a positive cytogenetic fragile X test result who are seeking further counseling related to the risk of carrier status among themselves or their relatives. (Cytogenetic testing was used before identification of the FMR1 gene and is significantly less accurate than the current DNA test. DNA testing would accurately identify premutation carriers and distinguish premutation from full mutation carrier women.)

Summary

Fragile X syndrome (FXS) is the most common inherited cause of intellectual disabilities and the most common genetic cause of autism. The genetics of FXS are complex, and there is a broad spectrum of clinical involvement across generations in families affected by fragile X mutations. A thorough family history, patient assessment, and genetic counseling should guide testing for individuals affected by the many manifestations of these mutations. Analytic sensitivity and specificity for diagnosing these disorders has been demonstrated to be sufficiently high.

There are a variety of ways management may change as a result of genetic testing. Evidence on the impact on health outcomes of documenting FMR1 gene mutations is largely anecdotal but may end the need for additional testing in the etiologic workup of an intellectual disability, aid in management of psychopharmacologic interventions, and assist in reproductive decision making. Therefore, genetic testing for FMR1 mutations may be considered medically necessary in individuals of either sex with intellectual disability, developmental delay, or autism spectrum disorder, and for other clinical scenarios outlined in the policy statements.

Practice Guidelines and Position Statements

American College of Medical GeneticsACMG’s Professional Practice and Guidelines Committee makes the following recommendations regarding diagnostic and carrier testing for FXS.(9) The purpose of these recommendations is to provide general guidelines to aid clinicians in making referrals for testing the repeat region of the FMR1 gene.

  • Individuals of either sex with intellectual disability, developmental delay, or autism, especially if they have (a) any physical or behavioral characteristics of fragile X syndrome, (b) a family history of fragile X syndrome, or (c) male or female relatives with undiagnosed intellectual disability.
  • Individuals seeking reproductive counseling who have (a) a family history of fragile X syndrome or (b) a family history of undiagnosed intellectual disability.
  • Fetuses of known carrier mothers.
  • Affected individuals or their relatives in the context of a positive cytogenetic fragile X test result who are seeking further counseling related to the risk of carrier status among themselves or their relatives. The cytogenetic test was used before the identification of the FMR1 gene and is significantly less accurate than the current DNA test. DNA testing on such individuals is warranted to accurately identify premutation carriers and to distinguish premutation from full mutation carrier women.

In the clinical genetics evaluation to identify the etiology of autism spectrum disorders, ACMG recommends testing for FXS as part of first tier testing.(1)

Academy of Pediatrics

AAP recommends that, because children with FXS may not have apparent physical features, any child who presents with developmental delay, borderline intellectual abilities, or intellectual disability, or has a diagnosis of autism without a specific etiology should undergo molecular testing for FXS to determine the number of CGG repeats.(5)

American Congress of Obstetricians and Gynecologists

ACOG (Committee Opinion, 2010) recommends that prenatal testing for FXS should be offered to known carriers of the fragile X premutation or full mutation, and to women with a family history of fragile X-related disorders, unexplained intellectual disability or developmental delay, autism, or premature ovarian insufficiency.(18)

 References:

  1. Schaefer GB, Mendelsohn NJ. Clinical genetics evaluation in identifying the etiology of autism spectrum disorders: 2013 guideline revisions. Genet Med 2013; 15(5):399-407.
  2. Miles JH. Autism spectrum disorders--a genetics review. Genet Med 2011; 13(4):278-94.
  3. Monaghan KG, Lyon E, Spector EB. ACMG Standards and Guidelines for fragile X testing: a revision to the disease-specific supplements to the Standards and Guidelines for Clinical Genetics Laboratories of the American College of Medical Genetics and Genomics. Genet Med 2013; 15(7):575-86.
  4. Hunter J, Rivero-Arias O, Angelov A et al. Epidemiology of fragile X syndrome: A systematic review and meta-analysis. Am J Med Genet A 2014.
  5. Hersh JH, Saul RA. Health supervision for children with fragile X syndrome. Pediatrics 2011; 127(5):994-1006.
  6. Nolin SL, Sah S, Glicksman A et al. Fragile X AGG analysis provides new risk predictions for 45-69 repeat alleles. Am J Med Genet A 2013; 161A(4):771-8.
  7. Yrigollen CM, Mendoza-Morales G, Hagerman R et al. Transmission of an FMR1 premutation allele in a large family identified through newborn screening: the role of AGG interruptions. J Hum Genet 2013; 58(8):553-9.
  8. Subcommittee on Attention-Deficit/Hyperactivity Disorder SCoQI, Management. ADHD: Clinical Practice Guideline for the Diagnosis, Evaluation, and Treatment of Attention-Deficit/Hyperactivity Disorder in Children and Adolescents. Pediatrics 2011; 128(5):1007-22.
  9. Sherman S, Pletcher BA, Driscoll DA. Fragile X syndrome: diagnostic and carrier testing. Genet Med 2005; 7(8):584-7.
  10. ARUP Laboratories. Fragile X ( FMR1 ) with reflex to methylation analysis, 2014. Available online at: http://ltd.aruplab.com/Tests/Pub/2009033. Last accessed May 2014.
  11. ARUP Laboratories. Fragile X ( FMR1 ) with reflex to methylation analysis, fetal, 2014. Available online at: http://ltd.aruplab.com/Tests/Pub/2009034. Last accessed May 2014.
  12. Grasso M, Boon EM, Filipovic-Sadic S et al. A novel methylation PCR that offers standardized determination of FMR1 methylation and CGG repeat length without southern blot analysis. J Mol Diagn 2014; 16(1):23-31.
  13. Gatta V, Gennaro E, Franchi S et al. MS-MLPA analysis for FMR1 gene: evaluation in a routine diagnostic setting. BMC Med Genet 2013; 14:79.
  14. Chaudhary AG, Hussein IR, Abuzenadah A et al. Molecular diagnosis of fragile X syndrome using methylation sensitive techniques in a cohort of patients with intellectual disability. Pediatr Neurol 2014; 50(4):368-76.
  15. Inaba Y, Schwartz CE, Bui QM et al. Early Detection of Fragile X Syndrome: Applications of a Novel Approach for Improved Quantitative Methylation Analysis in Venous Blood and Newborn Blood Spots. Clin Chem 2014.
  16. Hawkins M, Boyle J, Wright KE et al. Preparation and validation of the first WHO international genetic reference panel for Fragile X syndrome. Eur J Hum Genet 2011; 19(1):10-7.
  17. Michelson DJ, Shevell MI, Sherr EH et al. Evidence report: Genetic and metabolic testing on children with global developmental delay: report of the Quality Standards Subcommittee of the American Academy of Neurology and the Practice Committee of the Child Neurology Society. Neurology 2011; 77(17):1629-35.
  18. American Congress of Obstetricians and Gynecologists. Committee opinion, number 469: carrier screening for fragile X syndrome, October 2010. Available online at: http://www.acog.org/Resources_And_Publications/Committee_Opinions/Committee_on_Genetics/Carrier_Screening_for_Fragile_X_Syndrome. Last accessed May 2014.

Codes

Number

Description

CPT   81243 FMR1 (Fragile X mental retardation 1) (eg, fragile X mental retardation) gene analysis; evaluation to detect abnormal (eg, expanded) alleles
  81244 FMR1 (Fragile X mental retardation 1) (eg, fragile X mental retardation) gene analysis; characterization of alleles (eg, expanded size and methylation status)
ICD-9-CM Diagnosis  299.00-299.01 Autistic disorder code range
  315.00-315.9 Specific delays in development code range
  317-319 Itellectual disabilities code range
  V18.4 Family history of intellectual disabilities
  V26.31 Testing of female for genetic disease carrier status
  V28.89 Other specified antenatal screening
ICD-10-CM (effective 10/1/15) F70-F79 Intellectual disabilities code range
  F80.0-F80.9 Specific developmental disorders of speech and language code range
  F82 Specific developmental disorder of motor function
  F84.0 Autistic disorder
  Z31.430 Encounter of female for testing for genetic disease carrier status for procreative management
  Z31.440 Encounter of male for testing for genetic disease carrier status for procreative management
  Z81.0 Family history of intellectual disabilities
ICD-10-PCS (effectve 10/1/15)    Not applicable. ICD-10-PCS codes are only used for inpatient services. There are no ICD procedure codes for laboratory tests.


Index

FMR1 Genetic Testing


Policy History

Date Action Reason
06/14/12 Add to Medicine -Pathology/Laboratory section Genetic testing for FMR1 mutations may be considered medically necessary for specific patient populations
6/13/13 Replace policy Policy updated with literature search through April 2013. No new references added. No changes to policy statements.
6/12/14 Replace policy Policy updated with literature review through May 31, 2014; references 3-4, 6-8, 10-15, and 17-18 added; reference 2 deleted; reference 1 updated. Policy statements and entire policy updated to reflect current DSM-V diagnostic categories, ie, “intellectual disability” replaces “mental retardation.” Policy statement on testing relatives of affected individuals reworded for clarity. Otherwise, no change to policy statements.