Optimized group sequential study designs for tests of genetic linkage and association in complex diseases

Association of LEPR gene polymorphisms with the risk of hepatitis B virus-related liver disease in Guangxi Chinese: A case-control study

BACKGROUND AND OBJECTIVE

Leptin receptor (LEPR) signaling inhibits apoptosis, promotes angiogenesis and proliferation, and plays a critical role in carcinogenesis. Variants of the LEPR gene may be key factors in the growth of human malignant tumors. However, the relationship between LEPR polymorphisms and hepatocellular carcinoma (HCC) has not been thoroughly investigated. Therefore, we further investigated the association between LEPR polymorphisms and the risk of chronic hepatitis B (CHB), hepatitis B virus (HBV)-related liver cirrhosis (LC), and HCC in a southern Guangxi Chinese population.

METHOD

Two LEPR polymorphisms (rs1137100 and rs1137101) were genotyped in 138 CHB patients, 136 patients with LC, 149 HCC patients, and 146 healthy controls using the SNaPshot method.

RESULTS

We did not observe any significant difference in the LEPR rs1137100 and rs1137101 polymorphisms between the groups of healthy controls and patients (all p > 0.05), regardless of genotypes, alleles, or haplotypes.

CONCLUSIONS

Our data suggest that the genetic variants of the LEPR gene are not associated with the risk of HBV-related liver diseases (CHB, LC, and HCC) in the Guangxi population. Further studies are necessary to validate these results.

The association study of calmodulin 1 gene polymorphisms with susceptibility to adolescent idiopathic scoliosis

Objective. Idiopathic scoliosis is the most common pediatric spinal deformity affecting 1% to 3% of the population, and adolescent idiopathic scoliosis (AIS) accounts for approximately 80% of these cases; however, the etiology and pathogenesis of AIS are still uncertain. The current study aims to identify the relationship between calmodulin 1 (CALM1) gene and AIS predisposition, to identify the relationship between the genotypes of the SNPs and the clinical phenotypes of AIS. Methods. 146 AIS patients and 146 healthy controls were enrolled into this case-control study. 12 single nucleotide polymorphisms (SNPs) candidates in CALM1 gene were selected to determine the relationship between CALM1 gene and AIS predisposition. Case-only study was performed to determine the effects of these variants on the severity of the condition. Results. Three SNPs from 12 candidates were found to be associated with AIS predisposition. The ORs were observed as 0.549 (95% CI 0.3519–0.8579, P = 0.0079), 0.549 (95% CI 0.3519–0.8579, P = 0.0079), and 1.6139 (95% CI 1.0576–2.4634, P = 0.0257) for rs2300496, rs2300500, and rs3231718, respectively. There was no statistical difference between main curve, severity, and genotype distributions of all of 12 SNPs. Conclusion. Genetic variants of CALM1 gene are associated with AIS susceptibility.

Including sampling and phenotyping costs into the optimization of two stage designs for genome wide association studies

We propose optimized two-stage designs for genome-wide case-control association studies, using a hypothesis testing paradigm. To save genotyping costs, the complete marker set is genotyped in a sub-sample only (stage I). On stage II, the most promising markers are then genotyped in the remaining sub-sample. In recent publications, two-stage designs were proposed which minimize the overall genotyping costs. To achieve full design optimization, we additionally include sampling costs into both the cost function and the design optimization. The resulting optimal designs differ markedly from those optimized for genotyping costs only (partially optimized designs), and achieve considerable further cost reductions. Compared with partially optimized designs, fully optimized two-stage designs have higher first-stage sample proportion. Furthermore, the increment of the sample size over the one-stage design, which is necessary in two-stage designs in order to compensate for the loss of power due to partial genotyping, is less pronounced for fully optimized two-stage designs. In addition, we address the scenario where the investigator is interested to gain as much information as possible, however is restricted in terms of a budget. In that we develop two-stage designs that maximize the power under a certain cost constraint.

Optimum two-stage designs in case-control association studies using false discovery rate

Genetic association studies using case-control designs are often done to identify loci associated with disease susceptibility. These studies are often expensive to perform, due to a large number of genetic markers. Several types of two-stage designs are proposed and used from the point of cost effectiveness. We proposed to control the false discovery rate for multiple-testing correction in two-stage designs, using optimal sample sizes and criteria for selecting markers associated with a disease in each stage to minimize the cost of genotyping. The expected power and cost of two-stage designs were compared with those of one-stage designs, under the assumptions that the genetic markers are independent and total sample size is fixed. The results showed that the proposed two-stage procedure usually reduced the cost of genotyping by 40-60%, with a power similar to that of the one-stage designs. In addition, the sample size and selection criteria, which are optimized parameters, are defined as a function of a prior probability that marker-disease association is true. So, the effects of mis-specification of a prior probability on efficiency were also considered.

GJB2 (connexin 26) mutations are not a major cause of hearing loss in the Indonesian population

Although hereditary hearing loss is a very heterogeneous disorder, variants in one gene, GJB2 (connexin 26), account for up to 50% of autosomal recessive nonsyndromal sensorineural hearing loss in most populations. This study investigates the contribution of GJB2 to autosomal recessive nonsyndromal hearing loss in the Indonesian population. We performed DNA sequence analysis in 120 patients with profound early childhood nonsyndromal hearing loss and in 100 control individuals and identified three novel variations resulting in amino acid substitutions (p.Gly4Asp, p.Thr5Ala, and p.Gly160Arg). Although we proved that p.Gly4Asp was not disease-causing, the pathological nature of p.Thr5Ala and p.Gly160Arg could not be determined. No recurrent disease-causing mutation could be detected in this Indonesian population. These findings are in contrast with the results obtained in other populations where GJB2 is a major cause of congenital recessive hearing loss.

Developmental Dyslexia – Recurrence Risk Estimates from a German Bi-Center Study Using the Single Proband Sib Pair Design

OBJECTIVE

Several studies have demonstrated a genetic component for dyslexia. However, both segregation and linkage analyses show contradictory results pointing at the necessity of an optimal ascertainment scheme for molecular genetic studies. Previously, we have argued that the single proband sib pair design (SPSP) would be optimal. The aims of this paper therefore are to demonstrate the practicability of the SPSP design and the estimation of recurrence risks for reading and writing.

METHODS

We assessed spelling and reading in a family sample ascertained through the SPSP design. 287 families with at least two siblings and their parents were recruited. At least one child was affected with spelling disorder according to a one standard deviation (1SD) discrepancy criterion.

RESULTS

Mean values for probands and their siblings were different for both the spelling and the reading phenotype. For the probands, variances of the phenotype spelling were smaller. These effects became stronger with more extreme selection criteria. Both siblings fulfilled the 1SD criterion for spelling and reading in 60.3 and 28.9% of the families, respectively, indicating a low cost efficiency of the double proband sib pair approach. A recurrence risk of 4.52 (CI: 4.07-4.93) was obtained for spelling when the 1SD criterion was applied to both siblings. Recurrence risk estimates were similar for reading.

CONCLUSION

The study demonstrates the suitability of the SPSP design for genetic analysis of dyslexia. The recurrence risk estimates may be used for determining sample sizes in gene mapping studies.

Design considerations in the sequential analysis of matched case-control data

A role for sequential test procedures is emerging in genetic and epidemiological studies using banked biological resources. This stems from the methodology's potential for improved use of information relative to comparable fixed sample designs. Studies in which cost, time and ethics feature prominently are particularly suited to a sequential approach. In this paper sequential procedures for matched case-control studies with binary data will be investigated and assessed. Design issues such as sample size evaluation and error rates are identified and addressed. The methodology is illustrated and evaluated using both real and simulated data sets.

Reducing sample sizes in genome scans: Group sequential study designs with futility stops

Group sequential study designs can greatly facilitate analyses of genetic linkage in complex traits. We recently proposed designs allowing stopping investigations early if the result is significant (König et al. [2001] Am. J. Hum. Genet. 69:590-600), thereby decreasing average sample sizes under the alternative hypothesis. However, average sample sizes were slightly increased under the null hypothesis. We now present designs where the analysis of markers is additionally stopped in case of futility, i.e., if the probability for significant results is sufficiently low. These sequential designs are applied to linkage analyses of single loci. We calculated sample sizes, time points, and critical boundaries for all analyses for 2- and 3-stage designs at an overall significance level of 0.0001. To confirm the validity of asymptotic approximations, Monte Carlo simulations were performed. The utility is demonstrated analyzing genome scan data provided for the Genetic Analysis Workshop 12. Application of the novel sequential designs yields tremendous decreases in average sample sizes, regardless of the size of the underlying genetic effect at investigated loci. Depending on the applied design, almost half of the sample size is spared on average. These enormous savings are expected to have a special impact on costs and time of large-scale studies such as genome scans.

Group Sequential Study Designs in Genetic-Epidemiological Case-Control Studies

OBJECTIVE

In past years, the focus of genetic-epidemiological studies has shifted to analyzing complex diseases. Here, single genes often contribute only little to the manifestation of traits so that many probands have to be included in a study to reliably detect small effects. To reduce the number of required phenotypings and genotypings and thus facilitate analyzing complex traits, sequential study designs can be applied.

METHODS

For sequential analyses of complex diseases in association studies, we compare the procedure by Sobell et al. (Am J Med Genet 1993;48:28-35) with the adaptation of formal group sequential study designs by Pampallona and Tsiatis (J Stat Plan Inf 1994;42:19-35). Error rates and average sample sizes are investigated by Monte-Carlo simulations.

RESULTS

Formal sequential designs have a higher power regardless of underlying genetic effects. In addition, compared with conventional designs with fixed samples, average sample sizes are reduced considerably; under the null hypothesis of no association, up to 50% of the required sample size can be spared.

CONCLUSIONS

To increase the efficiency of genetic-epidemiological case-control studies, we recommend using formal group sequential study designs. The tremendous savings in average sample sizes are expected to affect both cost and time spent on large-scale studies.