Incontinentia pigmenti: report on data from 2000 to 2013

We report here on the building-up of a database of information related to 386 cases of Incontinentia Pigmenti collected in a thirteen-year activity (2000–2013) at our centre of expertise. The database has been constructed on the basis of a continuous collection of patients (27.6/year), the majority diagnosed as sporadic cases (75.6%). This activity has generated a rich source of information for future research studies by integrating molecular/clinical data with scientific knowledge. We describe the content, architecture and future utility of this collection of data on IP to offer comprehensive anonymous information to the international scientific community.


Introduction
Incontinentia pigmenti (IP; OMIM#308300) is a rare multisystemic genomic disorder with an estimated prevalence at birth of 0.7/100,000 [1]. IP is X-linked and usually lethal in males, and affecting the skin, but also other neuroectodermal tissues, in females. The skin lesions are the first clinical manifestations that appear, starting in the neonatal period with a vesiculobullous eruption (Stage I) and following a three stage evolution varying in duration from months to years, namely a verrucous stage (Stage II), a hyperpigmented stage (Stage III), and finally a hypopigmented stage (Stage IV) usually continuing throughout life [2,3]. Such skin defects, that follows Blaschko lines, are always present in IP and are therefore considered the main diagnostic criteria for IP according to Landy and Donnai (1993) [2]. The severity of the disease is related to the presence of neurological and/or ocular impairment [4]. Overall, the prevalence of functional Central Nervous System (CNS) manifestations is approximately 30% [5,6] ranging from a single-seizure episode to severe motor and intellectual disability [7]. Ophthalmologic abnormalities are present in approximately 20%-37% of IP patients [5,6,8]. IP is due to a mutation of the X-linked IKBKG/ NEMO gene (Inhibitor of Kappa polypeptide gene enhancer in B-cells, Kinase Gamma/Nuclear Factor κB, Essential Modulator, GenBank NM_003639.3, OMIM#300248). Most cases have a recurrent deletion (IKBKGdel or NEMOdel4-10), removing exons 4-10 of the IKBKG/ NEMO gene. Non recurrent genomic rearrangements in the IP locus and point mutations in the IKBKG/NEMO coding region have also been reported [9][10][11]. IKBKG/ NEMO encodes for NEMO/IKKγ a regulatory subunit of the Inhibitor of the kappaB (IκB) Kinase (IKK) complex required for the canonical NF-κB pathway activation involved in many fundamental physiological and pathological functions [12,13]. Most IP female patients present with a skewed X-inactivation. The X-chromosome linked IKBKG/NEMO mutation causes an unbalanced X-inactivation in female IP patients [14], as in other X-linked diseases [15,16], because the absence of the NEMO/IKKγ protein makes the IP cells more sensitive to apoptosis [9]. In males, the extensive apoptosis is responsible for their early fetal lethality [17]. Occasionally, male patients with IP have been reported. They have shown the characteristic skin lesions observed in females and presented a postzygotic mosaicism for the IKBKG/NEMO exons4-10 gene deletion [18]. IP has also been diagnosed in males with a 47,XXY karyotype (Klinefelter syndrome) [19]. The large heterogeneity of defects, the severe clinical presentations, and the wide spectrum of IKBKG/NEMO alterations [7,11,14,20] makes the selection of homogeneous groups of patients difficult, precluding any therapeutic approaches. Indeed, despite the considerable progress that has been made in detailing the basic pathology of the IP disorder, the gap between research and clinical care has remained wide. Moreover, the paucity of patients collected at each single diagnostic centre makes an overall epidemiological report difficult. The integration of scattered resources may be crucial for the success of future scientific accomplishments.

Methods
Here, we report the setting up of a central data repository relating to a cohort of IP patients, the data having been collected in a 13-year-long experience (2000-2013) at our Italian centre of expertise for the molecular diagnosis of IP [21]. The IP patients included in our study have been selected on the basis of the Landy and Donnai (1993) [2] diagnostic criteria, and they also meet the most recently updated IP criteria [22]. We have constructed the first platform for the integration of molecular and clinical data on IP patients. Our sample comprises 386 patients (261 from Italian, 105 from European and 20 from non-European clinical centers), with an annual average of 27.6 new cases of IP diagnosed per year ( Figure 1).
All the clinical information has been obtained for each patient through their completion of a clinical IP questionnaire developed by the Incontinentia Pigmenti International Foundation (IPIF, [http://www.ipif.org/ ip_consortium.html], further extended by the France Incontinentia Pigmenti association (FIP, [http://incon tinentia-pigmenti.fr/]) and by the Italian ASSociation of Incontinentia Pigmenti (IPASSI, [http://www.incontinen tiapigmenti.it/]). A clinical IP questionnaire is available upon request from these organizations. We have integrated the clinical data with molecular diagnosis results for the IKBKG/NEMO alteration, by way of a well-standardized protocol [10,14,23]. The technical development of the register has involved significant preparatory work consisting in the building up of an in-house electronic database which is comprehensive and permissive, and which has a flexible structure able to register in an anonymous form the pool data from the patients. We have assigned one record to each IP sample, registered with a pseudonymous code. Each record has three domains: the pedigree, the clinical and the genetic domain. The Web domain will be available at link [http://www.igb.cnr.it/ipgb]. The data are not accessible to everyone but only to authorized users through the use of a protected password. A data-mining interface has been developed to ensure maximum flexibility so that users can perform any search they want using the "search" button placed in the homepage after the "log in". It is possible to perform multiple searches at once. To make the database permissive and flexible the first page contains only the three domains set.

Results
The pedigree and clinical information are available for 308 IP cases, while the genetic data are available for 193 samples, respectively ( Table 1). The pedigree domain contains more detailed entries accommodating the family data, for example the presence of an IP mother, sister, or grandmother, indicating the inheritance of the disease. We have registered 233 sporadic cases (75.6%) and 72 familial cases (23.4%) in our IP cohort.
The clinical domain consists of seven clinical items, one for each aspect of the phenotype presentation: "Skin defects", "CNS defects", "Ophthalmologic defects", "Teeth defects", "Hair defects", "Fingernail defects" and "Developmental evolution". A drop-down menu has been assigned to each item that, in most cases, contains details about all the specific alterations affecting the tissue, and, in addition, an open space for the annotation of novel clinical features. For example, the item "Skin defects" contains a drop-down menu indicating the stage of the IP skin abnormality, the age of onset, the type of alteration, and the region of the body in which the alteration is present. We report that the most frequent first symptoms leading to diagnosis, typically skin alterations (Stage I), appear before the first year in 99% of cases. The second stage and the third stage are reported within the first year in 96.6% and in 82.8% of cases, respectively. After this date the fourth stage is generally present ( Table 2). The specific frequency of each IP specific neuroectodermal defect observed in our cohort is shown in Table 1. CNS abnormalities were present in 31.5% (Table 1). In 17 cases, these were diagnosed by magnetic resonance imaging ( Table 3).
The genetic domain of the database contains four items: "NEMOdel4-10", "IKBKG/NEMO point mutation", "IP locus rearrangement", and "No known alteration found" ( Table 1). The mutation names comply with the accepted guidelines proposed by the Human Genome Variation Society [www.hgvs.org/mutnomen] [24]. The genetic domain reveals that 75.1% of patients have the NEMOdel4-10 deletion, 22.1% have an IKBKG/NEMO point mutation, 3.6% have an extended deletion in the IKBKG/NEMO locus, and 4.7% have no known alteration in the IP locus (Table 1). Finally, in each domain (pedigree, clinical, and genetic) an additional item, named "Supplementary Information", records in the database any supplementary data from the patient and his/her family when these are available (examples: presence of miscarriages; presence of nonpathogenic alterations in IP locus [25] such as deletions or point mutations in the NEMO pseudogene).